Seth Mydans, Jakarta – Top military commanders have won a skirmish in Parliament to slow their retreat from political influence. At the same time, they seem to be losing control of many of their troops in the field.

Since the forced resignation in May 1998 of President Suharto, who used the army to enforce his dictatorship, the military has given ground steadily to an overwhelming nationwide demand for its withdrawal from politics.

But without the strong control of Mr. Suharto, military experts – as well as Defense Minister Juwono Sudarsono – warn that in some places the chain of command has broken down. As a result, some rogue units are fighting their own small wars and pursuing their own economic interests.

With the close of a special parliamentary session last week, attention focused on a back-room maneuver by the military's legislative bloc that allowed it to hang on to a few of its allotted seats for an extra five years, until 2009.

The concession drew an outcry from critics for whom the political withdrawal of the military is important to ending the abuses of Mr. Suharto's 32-year rule.

But military experts said the concession seemed a mostly token move, probably amounting to a dozen or so seats – down from the military's current 38 seats and from the 75 they held under Mr. Suharto in the 700-seat legislature.

In fact, military influence throughout Indonesia has already been sharply reduced. Serving officers can no longer hold the political and administrative positions through which they virtually ran much of the country.

And apart from some renegades and influential retired generals, for most officers the main dispute now is whether to seek rapid or gradual reform, the experts said.

Indeed, said Salim Said, a political scientist who studies the armed forces, many officers, particularly in the younger generation, oppose the extension of the military's role in Parliament and continue to lobby against it.

More worrisome, the experts said, the weakening of central control has contributed to military abuses in the religious fighting in the Maluku islands, the separatist wars in the provinces of Aceh and Irian Jaya, the continuing tensions along the border of East Timor and a number of other places.

"There's no chain of command in Ambon," a Western diplomat said, referring to the main city in the Malukus. "In a way, the president does not have control of the military. We are almost seeing the beginnings of a breakdown in the state if this were to happen in many places. The same thing is happening in West Timor."

It was unsettling to many people last month to see President Abdurrahman Wahid reminding a military gathering of the fundamentals of their duty: "You must obey your commanders and your commanders have to obey the supreme commander, and that is the president."

The breakdown in the chain of command in the Malukus "is one of the most serious problems we are facing," said Mr. Juwono, the defense minister. "We have problems with ambiguous loyalty at various levels of the police and the military, simply because they have been there too long and have become participants."

Military reform has two aspects, said Harold Crouch, an Australian expert on the Indonesian military. "One, withdrawing from politics, is going reasonably well," he said. "The second is professionalization of the armed forces, and that is a different picture. What Indonesia desperately needs is a professional force especially trained for dealing with ethnic, religious and that sort of violence, and that is precisely what they don't have."

The problems are in military training and in poor pay and supplies, he and other analysts said. The Maluku islands are a clear example, where military units have taken sides in the conflict and in some cases are fighting each other. According to current estimates, more than 4,000 people have died since January 1999 in a local war between Christians and Muslims.

"The problem there is that the military is not well equipped and the commanders cannot control their troops if they cannot provide for them properly," said Mr. Said.

Because of their low pay and poor supplies, Mr. Crouch said, the military in the Malukus has been broken into small units that are billeted with local residents. "If the Christian side attacks a village and some Muslim troops are there, naturally they'll fight, and vice versa," he said.

But the problem runs deeper, to the low pay that has caused the Indonesian military to live off the land as it carries out its nationwide political and security roles. Local commanders run businesses and protection schemes and are deeply involved in illegal logging, mining and other activities.

And individual soldiers hire themselves out in all sorts of jobs, Mr. Crouch said – "illegal, semi-legal, a-legal and occasionally some legal jobs like bodyguards."

Now with conflict erupting around Indonesia's archipelago, the military is being called on increasingly to act as a peacekeeping force. "So you send them into a real battle zone and they are just not prepared for that sort of thing," Mr. Crouch said. "They are still thinking, 'How can I make more money? I'll sell my bullets to people, or something.' When you send in peacekeeping troops and they go selling their arms to the combatants, what do you do?"

Beyond selling weapons, the military continues to be involved in abuses around the country, partly, he said, because it is the only way they know of asserting their authority.

"In the first 30 years of Suharto, they didn't care," he said. "If there was a problem, shoot them up, beat them up, torture them, kill them, it didn't matter. There was no investigation. It even goes back to Dutch colonial times. If one of your people gets shot, you go to the nearby villages and burn a few houses and shoot a few people."

This has given rise to one of the strangest elements of military jargon to be found here, "emotion" as it refers to military activities.

In East Timor, in Aceh and in the Maluku Islands, when troops have run amok, their commanders have shrugged their shoulders at the strange ways of fighting men and explained, "Oh, they have become emotional."

To Mr. Crouch that is one of the most telling signs of the lack of professionalism in the Indonesian military, from top to bottom. "Professional troops might have emotions," he said, "but they keep them inside. That is the job of professional troops, not to become emotional."

What is most troubling, he said, is that their senior commanders seem to find the emotions of their men a satisfactory military explanation for mayhem.