Jun 14, 2024 Last Updated 8:34 AM, May 27, 2024

Lessons learned from Indonesia’s conflicts: Aceh, Poso and Papua

Sidney Jones lecture

Herb Feith Annual Memorial Lecture 2014

Sidney Jones

Three conflicts which the Indonesian government has tried to solve offer some sobering lessons for the country’s next president. A peace agreement in Aceh stopped an insurgency but the former rebels proved to be bad political leaders. An agreement in Poso stopped Christian-Muslim fighting but left an extremist network in place which continues to operate. A new policy unit was set up for Papua that failed by concentrating only on economic development, while initial steps toward dialogue with Jakarta seem stalled. Jones examines the reasons for these outcomes and what a new government might try going forward.

Edited transcript of lecture, Melbourne, 20 August 2014

I want to talk about the way the Yudhoyono government, the current government, has looked at and dealt with some of the key conflicts in Indonesia and what this means and what lessons it will have for the incoming government. Just to quickly place these three conflicts on a map: Aceh is at the tip of Sumatra; Poso, Central Sulawesi is in the middle of the country and Papua is at the easternmost end of the archiplelago.

The Yudhoyono government came into office determined to resolve some of these conflicts, one of which, in Poso had already had a peace agreement in 2001 before he came in, but Aceh was very much the jewel in the crown. This was a conflict that President Yudhoyono hoped he would get the Nobel Prize for, it was also a conflict on which his Vice President Jusuf Kalla—now again to be VP—did most of the work. The problem was that once the peace agreement was signed, it was almost as though Jakarta forgot about it and moved on to other things, believing it was and would remain a success. Now that jewel is somewhat tarnished. 

Poso had been a communal conflict where intense fighting took place between Christians and Muslims between 1998 and 2001, reaching a peak in 2000. It was resolved in a peace agreement that Jusuf Kalla also brokered in 2001. But what it left behind was a network of extremist cells initially mostly associated with the group Jemaah Islamiyah (JI) but which went on to become what you might call the symbolic centre of ISIS in Indonesia, where the local commander, a man named Santoso, has sworn an oath to ISIS and is clearly in communication with people in Syria.

Papua is the conflict that defies resolution. It's a conflict that Yudhoyono tried in different ways to address. It's also a conflict that may get some attention from Jokowi but it is a much, more difficult proposition.

Each of these presents problems for the incoming president and I don't have any doubt at all that the Constitutional Court will decide against Mr Prabowo. Jokowi will be the next president, and I think that's a very, very good thing.

Jokowi starts with a reservoir of goodwill in the conflict areas both in Aceh and in Papua. Poso is not yet very high on his agenda, but I think it should be, for a variety of reasons. Even with that goodwill and even with Jusuf Kalla as his Vice President I think that we will see some of the old guard in Jokowi's party presenting obstacles to any efforts to further the peace processes. 


I think as we look at Aceh it is important first to look at what made peace possible. I have just come back from a short trip to Myanmar and people are looking at Aceh as a model for everything. They are looking at it as a model to resolve the conflict in Kachin state; it was being presented as a model to resolve the southern Philippines, before that area developed its own very distinct path to peace, and for southern Thailand. But in fact the circumstances in Aceh were probably not replicable. For one thing it had factors which made it easier to solve than many conflicts: the insurgents themselves were ethnically relatively homogeneous; there were clear geographical boundaries to the contested territory; the potential spoilers to peace, especially in the military and among some of the conservative nationalists, were politically manageable; there were no other competing insurgencies that would cause a problem; and the Free Aceh Movement (Gerakan Aceh Merdeka, GAM) had a relatively unified leadership. But also we had three factors that actually made the peace process work at the time it was undertaken.

For one thing we had had military operations since 2003 which made GAM want an exit strategy and that was critical. We also had a new government come in with Yudhoyono in 2004 that wanted to make a difference and this was an opening to do so. And finally of course we had the tsunami which made both sides want to ensure a peace so that the rebuilding could take place. The convergence of these three factors—a change in the political calculus, a change in the military calculus and a dramatic game changer of another variety—are absent in other conflicts where Aceh has been proposed as a model, but it is interesting to keep in mind that these are what made it critical peace agreement both achievable and enduring.

The problem is that since the peace, Aceh has become in some ways a one-party state led by a GAM political party called Partai Aceh (PA) and it is causing some problems. The recent elections have given us a little glimmer of hope in terms of reducing that party’s support - but it's worth looking at how the peace process itself brought these problems into being. One was that it effectively left behind the GAM military structure in the form of an organisation called the KPA. The KPA is basically the old military structure of GAM, the commanders of which are in many cases the power behind the elected officials; they are used as the machine for getting out the vote. They are still involved in many areas in corruption and extortion and in some cases they have turned from trading in guns to trading in drugs. So in some areas the ex-GAM commanders have turned into what has become a little mafia in Aceh.

At the same time one of the critical points of the peace agreement in Aceh was a clause that allowed local parties to form in Aceh. This was different from any other province in Indonesia where political parties have to be national in scope, with a presence in more than half the provinces. There is no provision for national parties that only have a limited geographic base. As a result GAM was able to form a party called Partai Aceh. It is this party which has made use of that military machine that is now called the KPA and while it does have a core base of popular support, it has also used both intimidation and fear-mongering tactics to win the vote. Basically it is saying 'we brought you peace. If you don't vote for Partai Aceh, there might be a chance of renewed conflict'. That has been a very effective message up until recently. This party went on to dominate both the provincial and district governments at both the executive and legislative branches and it won with margins that seem incredible, with 75 per cent and 80 per cent in some districts in the Acehnese heartland along the east coast. It also won the election for governor in 2012. It has produced an interlocking political directorate where now the party called Partai Aceh and the head of KPA and the government are all interlinked in one man, Muzakir Manaf, who is concurrently the Vice Governor, the head of the party and the leader of the KPA.

The 2014 legislative elections show us, however, that Acehnese voters are beginning to push back. I had thought that Partai Aceh was so much in control of the government at both the executive and legislative branches and of institutions like the election commission that it wasn't going to be possible for the Acehnese to remove Partai Aceh by democratic means. Now it looks like it just might happen, although it may take another election cycle. So not this time round, but perhaps in five years.

Also, we had a very interesting split within PA where the vice-governor, Muzakkir Manaf, took the side of Prabowo in the presidential elections and made an alliance with Prabowo's party, Gerindra. Aceh’s governor, however, decided to go with Jokowi because he was so grateful for Jusuf Kalla's role in the peace process before and Kalla was running on the opposing ticket. So we had the PA split between the governor and the vice-governor. Actually I think this is a good thing, because I think we were in danger of having a one-party state perpetuate its rule. Now with the combination of the split within the party and the decline in PA support among the population more generally, it may be that we end up with a more competitive and democratic political atmosphere.

I think there are some serious questions for the Jokowi government in Aceh moving forward, because PA correctly maintains that not all of the Helsinki Peace Pact provisions have been fulfilled. Among the provisions that haven't been fulfilled are provisions that would increase the authority of the Aceh government, as well as the income of the Aceh government. The question for Jokowi is, how to you increase the autonomy of Aceh without at the same time strengthening what is already a very authoritarian party? Also, in Jakarta, especially in the Home Ministry, there is a tendency to see Aceh and Papua as just like any other province, except with a little more revenue. It is as though Special Autonomy doesn't really exist. They see these provinces as almost the same as any other province, with a couple of additional clauses. What is happening is that there are now proposals to have Bali become a province with Special Autonomy, and there is a campaign in Makassar for South Sulawesi to be given Special Autonomy. If you give Special Autonomy to everybody then what is special about Aceh and Papua? In short, Jokowi will have his work cut out for him trying to address the many issues around Aceh and Papua and regional autonomy.


As noted at the outset, Poso is an area which is an ongoing problem even though it has been off the radar screen until very recently. Once the peace agreement was signed there, it was as though the government pretty much forgot about Poso. Peace deal done, no more problems. The problem was from 2001 until 2007 we had a network of extremist cells continuing to engage in attacks, mostly on the Christian community, but in some cases on suspected informers, and this led to a situation where we saw crimes of an increasing level of brutality. They culminated in the bombing of a market in the Christian town of Tentena that killed 22 people in May 2005 and the beheadings of three schoolgirls the following October. It was the killings of the girls that finally triggered central government action, and a special police unit was set up. The police managed to catch the perpetrators and by January 2007, after a shootout between the police and militants and the arrests of the ringleaders of the network, it looked like extremism in Poso was finished. In fact, the clash ended the violence in Poso, but only temporarily.

In 2010, all of the extremist groups still committed to jihad in Indonesia, and there were about seven, decided to start a militant training camp in Aceh with the idea that this could become a nucleus of an Islamic community. They thought, foolishly, that the fact Aceh was the one province that could apply syariah meant that this project would have support from the Acehnese community. (In fact Acehnese, while deeply devout, have never been sympathetic to religious extremists.) Jemaah Islamiyah was the one major jihadi group that did not take part in the camp; after that shootout in Poso in 2007, JI decided it would no longer engage in violent attacks in Indonesia. All the other militant groups accused it of abandoning jihad, including in a video produced to raise funds for the camp. But in early 2010, the camp got broken up by the Indonesian authorities. Because of all of the arrests and some deaths of militants that took place during mopping up operations that followed, the target of terrorists shifted almost overnight from foreigners—tourists in Bali, people staying in big American-named hotels—to the police, with the main motivation being revenge. But many involved directly or indirectly in the camp managed to flee, creating new networks and new extremist cells. Where did they go?

Some of them went to Kalimantan and some of them went back to Poso. Also, in Poso some of the remnants of the extremist networks there decided that if the Aceh camp didn't work out, then maybe they should start a regional training centre in Poso. The key figure in this new effort was an ex-JI man who knew several of the fugitives from Aceh and in some cases offered them refuge. In late 2010, Santoso set up a military wing of an organisation that Abu Bakar Ba’asyir first started in 2008 called Jamaah Anshorut Tauhid (JAT) and then went off on his own. He was always someone who didn't like authority very much. He didn't like to be under JI and eventually didn't like to be under JAT. But he was very happy starting his own organisation called the Mujahidin of Indonesia Timor or MIT. This was an organisation which attracted support from a group in Makassar, from groups in Bima in Sumbawa, from Java, from Medan and elsewhere. Some of the same groups from elsewhere in Indonesia that sent recruits to the Aceh camp began going to Poso for training. More importantly, Santoso has become the nerve centre of the extremist network in Indonesia. He is somebody who was in communication with the Global Islamic Media Front (GIMF) of Al Qaida which was operating out of Waziristan, and more recently he is the person who was the first to take an oath of allegiance to ISIS. We have seen members of his network, people who have trained in Poso, lead some of these oath-taking ceremonies across Indonesia today. 

The questions that Poso raises are not just about how will Jokowi handle terrorism. I think that is an issue but I think the Poso case raises some other issues as well. One of them relates to police reform. Had the police been operating as a community police force in Poso from the day the peace agreement was signed in 2001, they would almost certainly have been able to pick up the fact that the network was lying dormant and was not dead. Even if they hadn't picked that up, after 2007 they certainly would have been able to document and monitor the ongoing regrouping of extremists that was taking place in Poso. The problem is that if the community does not trust the police, it means that people are never going to report suspicious circumstances. The old adage in Indonesia is that if you report a loss of a chicken to police you lose your kerbau (water buffalo). This notion of the police as abusive and corrupt isn't unique to Poso. Police reform and a focus on improving policing could make a huge difference. 

Secondly, how do you get better law enforcement without cutting back on civil liberties? This is an issue that every government around the world faces, but when dealing with extremism it becomes a particularly important issue. Indonesia probably has all the laws it needs to deal effectively with extremist networks: the question is, can it do so without abuse of the laws that were once used by the Suharto government to try to curb dissent? These include the criminal code provision against spreading hatred and criminal incitement (penghasutan). Both could usefully—and carefully—be used against extremist clerics known to be recruiting young men into organisations that use violence. The difficulty is how to ensure they are not misused, as they were in the old days.

Thirdly, how do you tackle the ongoing hostility between the police and the military? Some have suggested that this rivalry is preventing the arrest of Santoso in Poso. We saw this tension erupt in 2013 with the killing in a Yogyakarta prison of four men linked to the police; the gunmen were from army special forces, Kopassus. It is a real concern and I think we are seeing some of this tension between the police and military play out in different areas of Indonesia. It is something that Jokowi as president will need to address if he wants to avoid local conflict in the future. 


That brings us to Papua. Papua is by far the most complex region, when we are talking about conflict, of any in Indonesia. It is not a single conflict. It is a series of conflicts, of multiple and overlapping tensions. According to the National Violence Monitoring System, separatism or the nationalist struggle for independence (depending on whose side you are on), probably accounts for 15 per cent, if that, of the total violence in Papua. In addition to the independence vs autonomy issue, we have tensions between indigenous people and migrants from elsewhere in Indonesia. We have tensions between the highlands and the coast, which played out very strongly in recent elections. One of the things that we have seen is the growing dominance of highlanders in politics, whereas in the past it was mostly the coastal areas that dominated. We have inter- and intra-clan struggles, often tied to local elections. We have land and resource disputes and some of these are increasing with the opening up of Papua to more agribusiness and mining. Of all provinces, Papua now has the highest rate of people being killed in local elections disputes. We have vigilantism, people taking the law into their own hands. It is also the area where we have one of the highest levels of domestic violence of anywhere in Indonesia. So this is not a peaceful place and it is not reducible to simply the struggle between pro-independence forces and the state. 

These two maps also show us how much another factor has come into play and that is the carving up of Papua into smaller and smaller units. When I first went to Indonesia it was one province then called Irian Jaya, and it was five districts. It became eight districts by 1999 and shortly thereafter began multiplying. Today it is 42 districts and two provinces. There are proposals in the Ministry of Home Affairs for three more provinces, Papua Selatan (South) may be the next one, though Papua Barat Daya is also a contender, and 30 more districts (kabupaten). There aren't the skills in Papua to be able to staff all these. It is going to bring in more migrants and exacerbate the migrant-indigenous tension. It is also leading exacerbating local election violence because many of these new divisions are along ethnic or clan line, and violence erupts when a majority clan pits itself against the next largest clan in the district for a struggle over who will become the bupati (district head). In several of the highland districts we have seen candidates call in armed groups to support them, sometimes the Free Papua Movement (Operasi Papua Merdeka, OPM) and sometimes former militia. Once you begin to use armed groups as basically 'guns for hire' in political disputes it changes the whole nature of the contest and again makes the conflict much more difficult to address.

The Yudhoyono government tried to address Papua with several specific policies, but it did so within very tight constraints. It decided it would try to resolve the Papua question without addressing any of the underlying political grievances. But it did acknowledge that Special Autonomy had failed to significantly improve the lives of Papuans and it set up this unit called UP4B (Unit Percepatan Pembangunan Provinsi Papua dan Papua Barat), which was a unit for the accelerated development of Papua and West Papua. Initially when the unit was set up, the people advising Yudhoyono did suggest that it be allowed to address political issues as well, including human rights issues and “rectification of history. At the very least, these advisers were prepared to consider looking at some kind of seminar or discussion of the events surrounding the 1969 Act of Free Choice and the possible release of political prisoners. But after an incident in May 2011 where a German tourist was shot by one of the radical groups in Jayapura, all political issues were suddenly off the table. It was thought that to begin to address political issues in the wake of that violence would be seen to be capitulating to violence. As a result UP4B, which had a lot of goodwill behind it at first, ended up not being able to achieve very much and eventually losing all credibility.

The government was also gingerly willing to entertain the idea of dialogue, on its terms. It did this after a group called the Papua Peace Network—a civil society driven group—began a process of consultations around Papua to try and address a question that has always come up when the issue of dialogue has arisen with central government, which is 'who speaks for Papua?'. The Network was an effort to create a unified voice among Papuans through these consultations so that everybody would agree on what the critical issues that had to be addressed in Papua were - from the historical rectification issue to the issue of discrimination and stigmatisation of Papuans to economics and development and so on. The problem was that the process went a little bit off the rails in July 2011, when it held a congress bringing in people from all across Papua. The leaders made a decision to name five people as negotiators who represented the Papua pro-independence diaspora, including people here in Australia. This caused a number of problems. The network had been set up with the idea that the endpoint of any dialogue would be increased autonomy, not independence, and the only reason the government was willing to entertain interaction with this group was that it wasn't a negotiation: the phrase Yudhoyono used was “constructive communication”. In other words, you can talk about a lot of issues but it was not and could not be, in the government's view, any kind of negotiation between two equal sides. So once the Papua Peace Network identified the five diaspora figures as “negotiators” (perunding), it basically ended any possibility that this process was going to move very far. It did succeed in generating a series of meetings with top level security people in Indonesia but little concrete ever came of it. However, since then the Papua Peace Network has presented a policy paper to Jokowi with some specific ideas about what can be done to take the process further, and we’ll see what happens. Jokowi has said he is open to the idea of dialogue and he also says that he is open to the idea of trying to lift some of the constraints on access to Papua.

Then we had a proposal for something called Enhanced Special Autonomy (Otonomi Khusus Plus or Otsus Plus). Otsus Plus was a proposal that the Yudhoyono government put forward on Papua to address complaints that a decade of special autonomy had failed to improve the lives of Papuans. It wasn't initially seen as anything particularly radical, but in the course of trying to think through how you would revise the 2001 Law on Special Autonomy in Papua, some Papuans, particularly a small group from Manokwari, in the province of West Papua, came up with a really interesting document. It was something that surprised everyone, because Otsus Plus had no credibility in the Papuan public at large. The governors who were talking about this with Jakarta never consulted with the populace and many civil society groups felt that since Special Autonomy had failed, what was the point of an amended law? But the Manokwari group came up with some of the most creative ideas proposed to date on what to do about education, about the migrant issue, about shared resources, about positive discrimination toward indigenous Papuans and so on. For example on education there were very clear incentives for getting teachers out to remote areas, likewise on health issues. On migrants there provisions for special identity cards for non-indigenous Papuans and for removal of people who didn't have them. There were also some really good provisions on protection of customary land. But when this went to Jakarta it encountered the same fate that other similar proposals have encountered in the past. A process of watering down the draft took place and also the two provinces did not see eye to eye on all provisions. The end result is that while a government-approved draft has been submitted to parliament in the waning days of the Yudhoyono administration, Special Autonomy Plus is probably dead in the water. It is probably not going to see the light of day before the Yudhoyono government leaves office. The question is whether there anything in that document prepared in Manokwari that might be followed through by the Jokowi government. It is not clear, but it is certainly worth trying.

I think if we are looking at initiatives in Papua that have some impact we have to look at the achievements of Dr Tito Karnavian, the chief of police in Papua who has recently stepped down. I don't think he gets much kudos from the pro-independence groups because he did crack down on pro-independence demonstrations. He also, however, did more than anybody else has in recent memory to reduce the other levels of violence in Papua and it underscored the fact that having a reasonably enlightened chief of police in Papua, as in Aceh or in Poso, can do a lot to not only deal with violence once it erupts but also prevent it before it takes place. One thing that he concentrated on was improving the practices of his own personnel. I am not sure how many of you are aware, but Papua is a place where poorly performing personnel are often sent as punishment. It means that frequently for military and police you get the dregs in Papua. The only way to improve police performance is to treat it as a prestige post, not as place of banishment. There was an attack on a police station in the middle of the central highlands and the police chief sent people there who were scheduled to be accepted into the Police Academy for Officer Promotion. He said 'you serve here for six months and then you are guaranteed a spot in the officers' school the next time around'. So serving in conflict areas became places where aspiring police officers could be sent and that was an important improvement. Also, he was willing to accept the possibility that not everything had to be worked through the formal law enforcement system, that you could use adat (customary) structures. Even if people committed crimes you could use traditional justice mechanisms as a way of resolving them, rather than creating more ill-will by trying to prosecute things through the formal legal system.

The problem is, as frequently happens in Indonesia, you get one reforming individual as you had with Sri Mulyani in the Finance Ministry, or Tito in Papua but once that person leaves, everything can go back to square one. The question is how does Jokowi not only try to initiate reforms but ensure that those reforms can continue even if the personnel change?

So what can Jokowi and Kalla do on Papua? I think Kalla in particular, has the idea still that he can take the Aceh model and apply it to Papua. He was trying to do this through the same team he had from Makassar as late as year and a half ago. Basically his formula for Aceh was this: you look for the people that have the arms, you try to get a ceasefire, you offer them some kind of compensation or incentive package to stay out of returning to conflict and you do something to pull back the Indonesian military forces. That is basically the formula that worked in Aceh. It doesn't work, or hasn't worked in Papua because as I say, not only is the insurgency a very small part of a very complex problem, but also the OPM is not unified in the same way that GAM was unified in the past. The behind-the-scenes efforts of Kalla during the Yudhoyono administration had no success at all. He may try again but his efforts may face the same fate.

As with Aceh, the problem with Papua is how to balance meaningful autonomy with oversight from the central government? For example, there is such extensive corruption in both Aceh and Papua that even though you have Special Autonomy, some of the really good work has been done by the National Audit Board to look at provincial budgets identify possible areas of malfeasance, and demand explanations. I think that kind of oversight is critical. If you are going to develop incentives for teachers, for example, you are going to have to have the cooperation of the central government. So autonomy shouldn't mean giving enhanced power to these two areas of Indonesia and perhaps others as well, and then just forgetting about it and saying what you do with the place is your own concern. There has to be more supervision from the central government at the same time there is increased autonomy. Police reform in Aceh is as important in Papua, as in Poso. The need to improve the social services infrastructure and alleviate poverty, indeed everything that motivated the creation of the unit for accelerated development in Papua, those things are important and do need to be addressed. But you have to tackle the economic issues and the political issues simultaneously or else you don't get anywhere.

Overall the lessons from these three conflicts are that for Aceh and Poso in particular, government attention doesn't end with a peace agreement. You've got to give sustained attention to these areas if you are going to use the peace process to encourage further development. In all three of these areas good policing is critical but also in all three the very tricky issue of balancing civil liberties has to be addressed. For Aceh and Papua, Special Autonomy needs to be strengthened but carefully, and Jokowi needs to understand why so many Papuans are so deeply disappointed by the last ten years.

There is no set formula that can be transferred from one area to another. Not even very many elements of the peace processes in either Poso or in Aceh will work in Papua; it is far more complex. But all three areas, which will need the concentrated attention of Jokowi, will benefit from continued development of democratic institutions. 


Sidney Jones (www.understandingconflict.org) is the Director of the Institute for Policy Analysis of Conflict (IPAC), which she founded in 2013 on the principle that accurate analysis is a critical first step toward preventing violent conflict. From 2002 to 2013, Jones worked with the International Crisis Group, first as Southeast Asia project director, then from 2007 as senior adviser to the Asia program. Before joining Crisis Group, she worked for the Ford Foundation in Jakarta and New York (1977-84); Amnesty International in London as the Indonesia-Philippines-Pacific researcher (1985-88); and Human Rights Watch in New York as the Asia director (1989-2002). She holds a B.A. and M.A. from the University of Pennsylvania. She lived in Shiraz, Iran for one year as a university student, 1971-72, and studied Arabic in Cairo and Tunisia. She received an honorary doctorate in 2006 from the New School in New York.

Read IPAC's newly released report The Evolution of ISIS in Indonesia

Listen to an audio recording of this lecture courtesy of the Herb Feith Foundation.

Inside Indonesia 118: Oct-Dec 2014{jcomments on}

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