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Indonesia threatens to become engulfed by violence. Religion, nationalism and feelings of victimization have triggered conflict across the immense archipelago. Clashes between Muslims and Christians have prompted calls for an Islamic jihad, or holy war. Some fear the breakup of the world’s fourth-most populous nation, one that sprawls across strategic shipping lanes. Yet, the Indonesian government seems incapable of stopping the conflagration. The paralysis must be overcome and the violence halted — without resorting to the repression that has characterized previous efforts to combat such outbreaks.

The Indonesian government always argued that granting independence or autonomy to one of its restive provinces would inspire demands for equal treatment from others. That concern has been born out in the aftermath of East Timor’s referendum and calamitous birth as an independent nation. Like-minded movements have become more powerful in the provinces of Aceh, the Malukus, Irian Jaya, Borneo and even Bali, the sun-dappled vacationer’s paradise.

The violence began in Aceh, where Muslim militants, who enjoy popular support, are fighting for independence. Because the state is rich in oil and mineral reserves, the Jakarta government is reluctant to let it go. Fighting there has claimed at least 300 lives, but the actual number of casualties could be much higher. Indonesian President Abdurrahman Wahid has said that the province could hold a referendum on its future, but no sooner than three years from now. That satisfies neither militants who want freedom, nor Indonesian nationalists who will countenance no further dismembering of their country.

The unrest in Aceh has been overshadowed in recent weeks by fighting between Muslims and Christians in the Moluccas, commonly known as the Spice Islands. There is long-standing antagonism between the two groups, and it exploded late last year. The government puts the number of dead at 1,800, but others say the number of fatalities could be three times as high. Badly outnumbered, the Christian community says that it is threatened with extermination and has called for foreign peacekeepers, an option that Jakarta says is not possible.

Despite the violence, the government has done little. Mr. Wahid charged his popular vice president, Ms. Megawati Sukarnoputri, with handling the Aceh situation, but she has been virtually invisible. Mr. Wahid has been faulted for devoting more attention to foreign relations than the domestic crises.

There is speculation that factions within the military see the unrest as an opportunity to regain the power they have lost since the fall of President Suharto. By this reckoning, doing nothing undermines the government’s credibility. After its mishandling of the situation in East Timor and subsequent calls for human-rights trials, the military should be wary of taking any action.

While the reasons for the military’s ineffectiveness are unclear, there is no doubt that Mr. Wahid and the armed forces are at odds, as evidenced by his dismissal last week of a military spokesman who had been highly critical of the government. That move prompted fears of a coup serious enough for the United States to warn the military to respect the government. A coup may depose the lawful government, but it will solve nothing over the long term: Unrest in Indonesia simmered throughout the Suharto years.

Now the situation threatens to explode. Thousands of Muslims have taken to the streets calling for a jihad and claiming that violence in the Moluccas is an attack on Islam. Even some moderate Muslims, such as Mr. Amien Rais, the speaker of the Parliament, have endorsed the call for armed action. With a population that is about 90 percent Muslim, the prospect of religious war has to be taken seriously. In the last few days, over a dozen churches have been burned on the island of Lombok. Mr. Wahid has promised harsh action against anyone who tries to do just that — and as a respected Muslim leader, his words carry weight with the faithful — but his room for maneuver is dangerously narrow as a result of his conflict with the military.

The temptation to come down hard will be difficult to resist. Worse, none of Indonesia’s neighbors is likely to complain. No one wants to see the country fracture, as it could trigger similar movements elsewhere, as well as add a dangerous element of uncertainty into the region. The prospect of Islamic fundamentalist governments sitting astride stretches of the Straits of Molucca is a security planner’s nightmare. Some measure of autonomy for the provinces is needed to quell the independence movements, but they may not be satisfied with that. Sadly, Mr. Wahid is now paying for his predecessor’s excesses, and the price promises to be high.

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