Jakarta – Transforming Indonesia's tarnished but powerful military into a modern defence force will be an uphill battle, even for its new pro-reform chief who took over this week, analysts say.

Air Marshal Joko Suyanto, who on Monday took over as chief of Indonesia's armed forces, has promised to keep the military out of politics and respect democracy and human rights, but larger forces than he remain at work, they say.

For decades under autocratic former president Suharto the military exerted enormous influence over civil affairs, ran its own sometimes illicit cash-generating businesses and was accused of blatant human rights abuses.

While the military lost its appointed parliamentary seats in 2004 as part of a package of democratic reforms, Australian-based military and politics analyst Bob Lowry warns that it is still an independent animal.

"You have this organism that acts in its own right," he told AFP. "Can the new chief dismantle that? No, he doesn't have the ability to do that. It has to be driven by government," said Lowry.

In particular, he said, the military's network of legal and illegal businesses – from airlines to logging companies – reaches into almost every sector of Southeast Asia's largest economy, and is a rich source of income for individual commanders.

President Susilo Bambang Yudhoyono, himself a former army general, is unlikely to want to deprive the military of its major source of funds, Lowry said. "If the president wants to be re-elected, then he doesn't want to make any more enemies than he has to," he noted.

At best, dismantling the businesses, estimated several years ago as providing up to 70 percent of the military's operational costs, will take at least a decade, says Riza Sihbudi, an analyst from the Indonesian Institute of Sciences. "The problem is, what can provide an alternative source of income for these generals?" said Sihbudi.

That's a difficult question, admits Defence Minister Juwono Sudarsono, who says he needs at least twice the current budget of 2.5 billion dollars to pay his troops properly.

The military's blighted human rights record, which includes allegations that they killed up to a quarter of the population in East Timor and thousands in Papua and Aceh, is one thing likely to improve under Suyanto, Sihbudi said.

But the military will still lobby hard to avoid being dragged before any future human rights tribunal, he warned. "It will be difficult to bring past cases to court, because he (Suyanto) is from the air force, but most of those involved are from the army," said Sihbudi.

The army has traditionally been the most powerful wing of the armed forces. With a peace deal in Aceh and Papua's simmering separatist conflict only sporadically flaring up, rights abuses could be dramatically reduced, especially if the military shifts focus to external threats.

But this is not on the forseeable horizon, Jakarta-based security analyst Ken Conboy told AFP. "Just because peace has broken out in Aceh, they're under no illusions that the current situation will hold," said Conboy, referring to the military's attitude towards last year's peace accord, which ended almost three decades of fighting in the province.

The military does still have valid concerns about the Free Papua Movement (OPM), a small disorganised force in remote eastern Papua, he said, while fighting between Christians and Muslims in Maluku and Sulawesi could erupt again.

"They still need to have a rapid reaction force to deal with other paramilitary forces which are beyond the ability of police patrolling, especially given the terrain: jungle and a harsh topography," Conboy told AFP.

Lowry and Sihbudi however said that the defence ministry should be formulating a new policy based on Indonesia's current peaceful conditions, perhaps looking at how the military could be better used to assist in natural disasters.

But Lowry conceded this was unlikely. "The defence ministry is just a post office for the military," he quipped.

Indonesia has been talking up potential arms purchases in recent months, saying it is considering buying a dozen submarines – up from its current two – before 2024, as well as more Sukhoi fighter jets from Moscow to join its current four.

Rather than flexing its muscles, Indonesia is simply trying to recover after enduring a US military embargo – which ended last year – introduced in reaction to rights abuses in East Timor as well as the 1997 economic crisis.

"They're just filling in gaps, trying to restore the capability that they had before the embargoes were in place," said Lowry.

He said however that neither the defence ministry nor the military appeared to have thought about how Indonesia would face future defence threats. "In terms of military capability, it doesn't have a policy. I don't know how they will cope with long-term reality," Lowry added.