Sidney Jones, Jakarta – Since President Soeharto resigned in May 1998, violence and conflict seem to have become part of Indonesian life.

We have seen bitter sectarian strife, now on the wane, in Maluku and Poso and attempts to provoke it elsewhere. We have seen an escalation of violence in Papua and Aceh, and it's going to take enormous good will on all sides to make the new agreement on cessation of hostilities in Aceh hold.

We've seen horrendous outbreaks of violence between the Dayak and Madurese ethnic groups in West and Central Kalimantan. We've seen mob violence against suspected criminals; physical clashes between student groups, gangs, and in some cases, whole neighborhoods; and a proliferation of unofficial security organizations run by thugs who extort, intimidate, and provide protection in the name of political parties, religious organizations, and businesses.

Finally, we have Bali and likely links to international terrorism. It's no wonder that nostalgia for Soeharto is on the rise.

From Jakarta to Medan to Makassar, the man whose fall was so welcomed at home and around the world in 1998 is now seen as being tough and decisive: One man said Indonesia never would have had a terrorist problem under Jakarta – Didor Saja! (He'd just shoot them!). "He was bad, but he was good," another person told me. At least we felt safe."

The worst thing people are willing to say about the man now is that he spoiled his children. But we need to remember that much of the turmoil we're seeing now has its roots in the authoritarianism and political controls of the Soeharto years.

We complain bitterly about the woeful lack of leadership in this country, but we have to remember that Soeharto deliberately emasculated political parties, nipped any threat to his leadership in the bud, and discouraged many of Indonesia's best and brightest from even thinking about going into government.

We have been shocked by some of the communal and ethnic violence that has erupted. But the tensions that fueled these outbreaks didn't just suddenly appear in 1998. They were simply kept out of sight by rigid insistence on acceptance of Pancasila, and controls on freedom of expression that prevented open discussion about the seriousness of the problem.

And they were exacerbated by some of the development policies that Soeharto pursued, particularly with respect to poorly thought – through transmigration projects, allocation of land-use rights, and the granting of forest concessions, all of which took place with a colossal insensitivity to local cultures.

We bemoan, or we did until the Bali investigation, the poor performance of the police in maintaining law and order, and the lack of military accountability. But both are a direct consequence of the Soeharto government's use of the military as its internal security apparatus. It left the police with little to do except collect money. And it left a military trained to see its own compatriots as the major threat.

I was in Cambodia in late 1992 when an Indonesian battalion was stationed there with UN Peacekeeping Forces. They and the Bangladeshis were probably the most popular battalions with ordinary Cambodians. They didn't drink or womanize, they were extremely polite, and they went out of their way to help the local community. It was an ABRI Masuk Desa program that worked. Why? Because Cambodians weren't the enemy, and the soldiers didn't perceive them as such. One consequence of using the army in an internal security role is that the enemy becomes your own people.

Soeharto left the justice system in a shambles, and even if there were the political will to reform it now, which there isn't, it would take decades to build up a truly professional cadre of judges and prosecutors. The lack of credibility of the courts has several consequences for conflict resolution:

• It weakens the legitimacy of government institutions more generally;
• It encourages people to take justice into their own hands;
• It encourages people to look for alternative legal systems.

The press here has given much attention to the way in which some aspects of Islamic law are increasingly being applied across the country. But almost more worrisome is the growth in demand for application of hukum adat, customary law, by ethnic groups that are dominant in particular subdistricts or districts. By definition, hukum adat is exclusionary; it privileges members of one ethnic group against another.

On the one hand, it is seen by many in the Outer Islands as an instrument to redress the arbitrary land seizures of the Soeharto years. On the other, its application could serve to heighten inter-ethnic tensions or tensions between indigenous groups and migrants. If there were a credible national legal system for resolving disputes, the demand for adat law would not be so potent.

The proliferation of "civilian auxiliaries" to the security forces, quasi-official organizations that get very close to goon squads, and other organized but non-governmental armed groups is another worrisome legacy of the Soeharto years. The New Order made systematic use of civilian militias in East Timor and in Aceh, during the DOM period.

It may have been a standard counterinsurgency tactic, but the result was deeper polarization of society in troubled areas, and less accountability of the government. It created Pemuda Pancasila, Pemuda Karya, and other youth groups to mobilize on behalf of the ruling party, Golkar, against the political opposition at election time.

These groups added to the culture of violence in Indonesia and set a precedent for the proliferation of laskars and satgas after Soeharto fell. The problem was that before, they all answered to Cendana. Now they answer to a host of different officials and entities at all levels of society, making it all the more difficult for a weak central government to rein them in.

The notion of civilian auxiliaries to the security forces, whether it's called Pam Swakarsa (military backed militia) or Kamra or a host of other possible names, is so ingrained that in discussions of police reform, the most common suggestion for building a bridge to a particular community is to create a Pam Swakarsa.

Not only do these organizations act as buffers between the police and the people instead of bridges, but they also quickly degenerate into simple proxies of the police – only with less training and no accountability. It's the police themselves, not their proxies, who should be bonding with communities.

Finally we come to terrorism. For a long time I resisted even the use of the word because I knew from my human rights background how easily it was misused, and how easily the term fit into sometimes dubious political agendas.

After Bali, I was more willing to use it here but I still think it's dangerously emotive. In any case, it's less easy to trace the development of some of the networks around Jamaah Islamiyah to specific policies of the New Order, but covert support to the revival of the Darul Islam movement in the mid-1970s laid the groundwork for some of what followed, and suppression of certain kinds of Muslim political discourse was probably a factor.

None of this is to let the post-Soeharto governments off the hook. It is too facile to say everything is the fault of the ancient regime. There have been more missed opportunities than one can count since May 1998 to bolster this country's political institutions and reduce conflict.

Jusuf Kalla deserves a lot of credit for putting together the Malino accords in Poso and Maluku and making them more or less stick, despite enormous obstacles. But if some of causes of violence are to be addressed, Indonesia will need more such risk-takers with a vision of Indonesia that goes beyond the city limits of Jakarta – and fewer spoilers.

The factors that brought Soeharto down – KKN or corruption, cronyism, and nepotism are alive and well as never before. The genuine post-Soeharto successes that Indonesia can point to, such as restoration of basic civil rights, constitutional changes leading to a direct election, the realignment of powers between executive and legislative branches of government, the big bang decentralization initiative – a success despite all the obvious problems – and popular excitement, once you get outside Jakarta, at the possibility of genuine political participation, should not be taken for granted.

These gains have to be protected and nurtured, and it's not happening. With all this in mind, let me turn to one success of this government that has been deservedly hailed as a major achievement-the agreement in Aceh on cessation of hostilities.

The roots of this conflict may lie in the distant past – Hasan di Tiro, leader of the rebel movement GAM, inevitably comes up with a letter from US President Ulysses S. Grant from 1864 to the Sultan of Aceh to prove the US once acknowledged Aceh as an independent country. Elements of the conflict go back to the Indonesian revolution and to the Darul Islam rebellion of the 1950s.

But much of the problem, and certainly its seeming intractability up until now, had its origins during the Soeharto years, and in particular, as a result of the counterinsurgency operations conducted from 1990 to 1998. The operations were a response to a real security threat – over a hundred GAM fighters had returned to Aceh from Libya and were making sporadic assaults on police and army posts.

But the heavy-handedness of the government response touched virtually everyone in Aceh, and led to a resentment against Jakarta that goes far beyond whatever support there is, and there's a lot, for independence.

I remember talking to one kyai in Uleeglee in 1991 who believed that it would be better for the guerrillas to surrender, and believed that if they did so, the government would make good on its offer of amnesty. He persuaded one young man from a family he was close to turn himself in. The man did so, and disappeared the next day. The kyai was anguished about the young man and felt thoroughly betrayed by the government.

After Soeharto fell, many Acehnese were convinced that some accounting for the DOM period would take place. Military and civilian officials apologized to the Acehnese for their suffering, promised justice, and nothing happened. And with newfound political freedoms, the anger and disappointment at the lack of concrete action led to organizing of proindependence groups, some of them close to GAM, in a way that we'd never seen before.

GAM also found the atmosphere more conducive and sent hundreds of fighters back from Malaysia. The military and police responded, and instead of the conflict easing, it worsened. Now, thanks to incredible persistence of the Henry Dunant Centre, the support of the international community, the work of Hassan Wirayuda, Soesilo Bambang Yudhoyono and their colleagues, and the general war-weariness of the Acehnese, there is a genuine chance for peace.

But it's only a chance, it's not guaranteed, and many of the factors that have contributed to conflict elsewhere in Indonesia will have to be overcome in Aceh. These include the many vested economic interests in the conflict, and those who are making the most profit from the war are unlikely to see the promised reconstruction aid as an incentive to make peace. Signatures on a peace of paper do not wipe out decades of distrust.

Many GAM members see their weapons as their only bargaining chip, and to turn them in is to lose that leverage; moreover, it remains very unclear what incentives the agreement gives GAM to participate in a political system that is as corrupt as the one in Aceh.

The huge concession made by the Indonesian government to allow international monitors is absolutely vital to the plan's success, and the Thai and Filipino soldiers will be warmly welcomed. (In East Timor, the Thai soldiers were a huge hit, not only because they provided medical services and ran a wonderful canteen, but because they taught kick-boxing to local youths!)

But the agreement is unclear on what ultimately happens if a serious violation is reported to the monitors, and what kind of efforts will be made to bring violators to justice.

The first few months of this agreement are going to be critical, as the implementing institutions are being set up. Expectations will be at their highest, and could fall the furthest if disgruntled parties make efforts, as they surely will, to undermine this accord. It is going to take an enormous amount of goodwill, attention, skill, resources, and leadership, on the part of all parties involved, to ensure that hostilities really do cease so that a process of peace-building can take place.]

The issue of accountability for past human rights abuses has been rightly deferred for the moment; the priority has got to be on ending the violence. But it can't be deferred forever. As we know from one conflict after another, if these issues are pushed to the side or buried, sooner or later they will come back to haunt us.

In closing, let me return to the issue of nostalgia for the Soeharto era. Indonesia is beset by more problems than any country in the world deserves, and it would take a miracle worker to solve them. But the biggest tragedy this country could face would be to turn its back on political and military reform.

Democracy is not the culprit here, and freedom is not the cause of conflict. The best strategy to protect this country from more sectarian strife, rebellions, and vigilante violence is to get reform back on track.

[Sidney Jones is the Indonesia Project Director or the International Crisis Group. This article was as speech presented on Tuesday at the 2002 Panglaykim Memorial Lecture in Jakarta.]