Sidney Jones – Indonesia continues to be plagued by astonishingly diverse forms of violence: vigilantism, communal conflict, armed insurgencies and counter-insurgency responses, terrorism, land and resource disputes, and shoot-outs between the army and police. That's not counting the occasional high-profile murder of a beloved public figure like Munir.

The challenges for Susilo Bambang Yudhoyono, also popularly known as SBY, are enormous. It's not as though Indonesia will disintegrate or become dangerously unstable if these problems are not solved.

But they could affect SBY's ability to deliver on promises of economic growth and restore investor confidence, and over the long term, if left to fester, they could lead to disillusionment with Indonesian democracy, which has had such a boost with the success of the 2004 elections.

At a more fundamental level, the basic human costs in terms of lost lives and livelihoods should be incentive enough to get some creative new policies into place.

But there are aspects of Indonesian violence that complicate policy formulation.

Each conflict or pattern of violence has its own constituency. For example, Indonesia's donors and some of its closest neighbors see terrorism as the No. 1 security challenge, not only because of terrorism's global reach – the fact that a meeting in Malaysia can lead to an operation in New York or training in Kandahar can lead to attacks in Jakarta – but also because foreign civilians are often targets.

In combating terrorism, the Indonesian police are the lead agency and have earned praise for their success in tracking down key suspects in terrorist violence, even if some very big fish remain at large.

But for most Indonesians, terrorism is not the main issue. Their own lives are touched far more by crime, or by land and resource disputes, than by bombings in Jakarta or Bali. Popular frustration at police passivity in the face of thug violence has led to vigilantism becoming a major problem – and causing hundreds more Indonesian deaths than Jamaah Islamiyah (JI) or like-minded organizations have done.

And local police often appear as the villains in clashes over land, as when they opened fire on farmers protesting the loss of their land to a rubber plantation in Bulukumba, South Sulawesi in June 2003 or when they were called in last month in Bojong, Bogor to put down a demonstration of villagers unhappy that their land was being used as a dump for metropolitan Jakarta's trash.

The reputation of the police may be rising in counter-terror quarters, but it appears to be sinking in the eyes of the public, if opinion polls are any indication.

This gulf in perceptions about which security issues matter most has two consequences. It is relatively easy for groups sympathetic to anti-Western violence to take control of the public spin, and portray moves to arrest terror suspects as persecution of Muslim activists – especially when ill-treatment or torture is alleged, and there appear to be some well-founded claims.

It also makes it much more difficult for the government to push ahead with any more energetic counter-terror program, because it runs the risk of being accused of capitulating to Western pressure.

The need is to bring the security concerns into better balance. Local grievances probably deserve more attention, together with improving police capacity at the local level and seriously investigating allegations of police abuse.

At the same time, the Indonesian public deserves a better, more thorough answer from the government to the question of why it should be concerned about terrorism than it got during the Megawati Soekarnoputri administration.

The constituency concerned about Aceh (Nanggroe Aceh Darussalam) and Papua is very different. Despite the enormous loss of life, particularly in Aceh, and the long duration of both conflicts, they have remained extraordinarily localized.

What goes on at extreme ends of the archipelago doesn't seem to have much of an impact on the middle, and the tight media controls and restricted access only add to the sense of remoteness.

But for the Indonesian military, unburdened by any major external threat, separatism towers above all else as a security concern, far higher than terrorism or communal conflict. Separatism poses the only genuine threat to the unity of the Indonesian state; therefore, in the views of many (but not all) TNI officers, military force is the only possible answer.

SBY has made it clear that he doesn't share this view, but it would be desirable to get some constructive alternatives on the table fairly quickly – particularly since the extension of the civil emergency in Aceh on Nov. 18 seemed to be sending the opposite message. The detention on corruption charges of Abdullah Puteh, Aceh's notorious governor, in early December opens some interesting possibilities for non-military steps: establishment of a transition administration, improving post-emergency governance, a new process of dialog with a much broader swath of the Acehnese population than has hitherto been the case, justice for the past, and renewed attention to the weaknesses of the Special Autonomy law.

But many Acehnese are tired of talk and are beginning to think that with the roll-over of the emergency, the ongoing media restrictions, and the lack of transparency in accounting for the cost of military operations over the last two years, they may be in for more of the same.

In Papua, the mood is much more upbeat, at least in elite circles. Despite the strange decision of the Constitutional Court, basically saying the division of Papua was unconstitutional, but the creation of West Irian Jaya would stand as a fait accompli, many Papuans appear to be optimistic that SBY will find a way to restore meaning to the idea of special autonomy.

The key here is the creation of a single Papuan People's Council (Majelis Rakyat Papua or MRP) that covers the entire territory as originally proposed by the Papuan drafting committee in August 2002 – not one MRP per province as the Megawati government came back with in late 2003. If SBY presides over the emergence of a workable MRP, he will have taken an important step toward addressing Papuan grievances. It will at least change the atmospherics for the better and buy time to put a longer-term strategy together.

Faced with so many different kinds of conflict and so many different constituencies involved, SBY would have a difficult time under the best of circumstances. Regional autonomy, decentralization and pemekaran (administrative fragmentation) add further layers of complexity.

But SBY also has opportunities, not to mention legitimacy, from a direct election that his immediate predecessors lacked. To turn those advantages to good use, he needs to have a team that can take a broad look at the range of ongoing conflicts and violence and ensure policy input from beyond the most vocal vested interests involved (getting a few anthropologists and resource economists with field expertise into the conflict areas in question would be useful).

It is also utterly critical that no one in SBY's administration be permitted to benefit from the corruption of public funds designated for conflict prevention or resolution, including funds for military operations, assistance to the displaced, or counter-terror training. A zero-tolerance policy here, and commitment to ensure that no agency stands above the law, will help him immensely as he tackles the harder political questions.

[The writer is the Indonesian Project Director for the Brussels-based International Crisis Group (ICG).]