Rajiv Chandrasekaran, Jakarta – When he assumed office in October 1999 as Indonesia's first democratically elected president in four decades, Abdurrahman Wahid sought to show the country's once-mighty military who was boss. He appointed the first civilian defense minister. He dismissed a general implicated in the destruction of East Timor. He replaced several regional army commanders and appointed reform-minded generals to senior posts.

But in recent months, top military commanders have dispatched a message of their own to the president. They have turned their back on reform efforts, delaying their retreat from politics and rejecting calls to open their budgets to public scrutiny. And in what some analysts call a significant erosion of civilian control, several generals threatened last month to quit if Wahid appointed an outspoken reformer as the army's chief of staff.

"It was a question of power," said Salim Said, a political scientist who studies the Indonesian armed forces. "The military showed that it can make a decision and force the president to accept it."

The relationship between military leaders and the soldiers who are spread across the sprawling archipelago is even more fractured. In the Moluccas, Aceh and other strife-torn provinces, the chain of command has almost broken down, with some soldiers mounting unauthorized operations and others taking sides in sectarian clashes, military analysts say.

The anarchy also has spread to the capital: Several rogue soldiers are suspected of participating in a car bombing in the parking garage of the Jakarta stock exchange in September that killed 15 people.

Controlling the military, from foot soldiers to four-star generals, is widely viewed as one of the most important – and most intricate – challenges facing Indonesia as it struggles to embrace democracy after more than three decades of authoritarian rule.

Although many analysts believe the armed forces are too weak and fragmented to mount a successful coup, they say that disorder in the ranks and the lack of clear civilian authority are severely hindering efforts to quell separatist and sectarian violence raging across the country.

"This is quite a dangerous situation," said Gareth Evans, a former Australian foreign minister who heads the International Crisis Group, a research organization that has been analyzing Indonesia's political transition. "Unless the civilian government very firmly takes the reins and embarks on a series of major institutional reforms ... you're going to have elements of the military continuing to cause problems."

During the 32-year rule of former dictator Suharto, there was little distinction between the government and the military. Believing that the military's contribution to the anti-colonial struggle in the 1940s afforded it special rights, Suharto, a one-time general, appointed officers as cabinet ministers, supreme court judges, governors and directors of state-owned companies.

Military officers were involved in every level of government, down to village administration. "The military has been politicized, not to serve the state and the people, but to serve the power-holders," a stern Wahid said at the armed forces' 55th anniversary celebrations last month. "The military has been used by individuals to further their own interests and this must stop."

In his first months in office, Wahid attempted to address his concerns, removing Suharto loyalists and other hard-liners from top posts, most notably firing the former armed forces commander, Gen. Wiranto, after he was found to be complicit in the devastation of East Timor by military-backed militia groups following its independence referendum last year. The president also ordered the appointment of reformist officers, including Lt. Gen. Agus Wirahadikusumah, one of Wiranto's most outspoken critics, to a key army command.

But in late July, senior generals who favor a far slower pace of reform lashed back, removing Wirahadikusumah on grounds he released the results of an internal audit that revealed widespread corruption by his predecessor and suggested that some military funds may have gone to fund Islamic vigilantes in the Moluccas.

Wahid attempted to return the fire by considering Wirahadikusumah to be the new army chief. But the outgoing chief, Gen. Tyasno Sudarto, would have nothing of it. He organized a meeting of generals and circulated a letter effectively opposing Wirahadikusumah's appointment that was signed by 45 of them. Several also reportedly threatened to quit if Wirahadikusumah got the job. Wahid backed down.

"One area where Gus Dur made significant inroads with reform was with the military, and now that is being completely reversed," said a senior Western diplomat in Jakarta, referring to Wahid by his nickname.

In Indonesian-controlled western Timor, the military has failed – despite repeated orders from political leaders – to disarm and disband the militia groups that were responsible for the mayhem in East Timor in the summer of 1999. In fact, rogue military units are suspected of doing just the opposite: Western intelligence officials believe they have secretly been arming and otherwise supplying militiamen so they can cross the border and attack the UN peacekeepers who are running the nascent state.

In August, the military brokered a deal with lawmakers to retain a block of seats in the country's top legislative body until 2009, five years longer than Wahid and other political leaders had wanted. Military officers also received an effective amnesty for many types of human rights abuses committed in the past.

Officers also have dug in their heels on another key goal of reformers: disclosing private business ventures that generate approximately 75 percent of the military's budget. Because there is no public accounting of those funds, critics say there is corruption and spending on programs that have not been approved by civilian leaders.

Military officials insist that they are committed to reform, but they contend the process must move gradually to generate support among the ranks. "These are big changes for the armed forces," said Lt. Gen. Agus Widjoyo, the army's chief of staff for territorial affairs. "We cannot be too hasty."

While foreign military analysts are highly critical of the army, they note that the Indonesian navy and air force, far smaller and less politically connected branches of the armed services, have been more committed to reform.

The United States, which cut military ties with Indonesia in the wake of the violence in East Timor, has attempted to promote changes within the navy and air force within the bounds of congressional restrictions on interaction with the Indonesian armed forces. This summer, US officials allowed Indonesian air force officers to observe a regional training operation in Thailand and sailors to participate in a joint humanitarian exercise with the US Navy.