Sian Powell – The Indonesian military has a toxic reputation, based on a long history of gross human rights abuses across the archipelago, particularly in Papua, Aceh and the former province of East Timor. Human rights monitors have regularly accused the Indonesian military, or TNI, of a mind-boggling series of crimes including extra-judicial executions, torture, assaults and arbitrary detentions.

Now, after a slow start, Indonesian soldiers have rolled up their sleeves to help in the Aceh disaster zone, carting corpses, trucking aid, and providing medical assistance. Yet even in the midst of the crisis, the accusations continue to fly, with claims the military has also been selling aid, hunting rebels and harassing villagers.

This has not surprised some military analysts, who point out that even though Indonesia has made progress on the political front, it will take time for the armed forces to become a modern and accountable fighting corps.

But with the world's media now busily nosing around Aceh, the Indonesian military is operating under the glare of the international spotlight.

The next few months or so will set the tone for the future, either helping to repair the force's diabolical reputation, or adding another chapter to a long tale of impunity.

The US banned sales of weapons and military equipment to Indonesia after the military opened fire on unarmed demonstrators at Santa Cruz cemetery in East Timor in 1991, killing as many as 271 people, and defence ties were cut further after the military and its militia proxies laid waste to East Timor and killed 1400 East Timorese in 1999. More recently, there have been US bans on military exchange and financing programs following the fatal shooting of two Americans in Papua in 2002. Australia, too, severed links with the military's special forces, or Kopassus, after the East Timor violence.

The tsunami disaster has started to warm relations that had already been gently thawing for some time. The Indonesian military is seen by many conservatives as a crucial ally in the battle against global terrorism and, since September 11, even allies with dirty hands have been keenly sought.

These supporters of renewed links, both in the US and Australia, believe the Indonesian military should be coaxed and bribed into behaving more humanely rather than castigated for its abuses. Indonesia's new directly elected president Susilo Bambang Yudhoyono, they point out, went to the US for part of his military education, and he is now making all the right noises about the importance of democracy and the rule of law. Yet activists retort that Australia's close military relations with Indonesia in the Suharto years did little to curtail the behaviour which culminated in the savaging of East Timor.

The military was general Suharto's enforcement agency, and for 32 years it was free to run Indonesia as it wanted: usually with brutality. Since Suharto was shoved from the presidency in 1998, Indonesia has become increasingly democratic, and the military no longer has an automatically allocated bloc of seats in parliament. Yet it still wields enormous power and allegations continue to be made of atrocities in conflict zones, including Aceh and Papua.

The Indonesian military launched a crackdown on separatist rebels in Aceh in 2003 and, up to the end of last year, more than 2000 suspected insurgents had been killed. For much of the crackdown, the province was closed to foreign diplomats, aid-workers and journalists, permitting the military to subdue the province as it saw fit. An Amnesty International report on Aceh, published last October, condemned the military's impunities in the blood-soaked province, as well as having a swipe at the rebels, or the Free Aceh Movement, for its crimes.

"It appears that little has changed in the way in which the security forces respond to both armed and civilian independence movements," the report said.

Young men, it went on, were frequently suspected of being rebels by the security forces, and were particularly at risk of human rights violations, including unlawful killing, torture, ill-treatment and arbitrary detention. Human Rights Watch made similar allegations in an earlier report on torture in Aceh.

Putting all that to one side, the cries to restore ties with the Indonesian military grow ever louder. On his recent visit, US Deputy Defence Secretary Paul Wolfowitz made it clear he backed renewed ties with the Indonesian military.

"We need to think about how we can strengthen this newly elected democratic government, strengthen the civilian Defence Minister ... to help build the kind of defence institution that will ensure in the future that the Indonesian military, like our military, is a loyal function of a democratic government."

The disaster has already changed the dynamic between Indonesia and the US. Following outgoing secretary of state Colin Powell's visit to Aceh, the US permitted Indonesia to buy crucial spare parts for its C130 planes needed for the relief effort.

The embargo on the sale of spare parts by the US for military aircraft had effectively grounded most of the Indonesian military's C130 fleet. Even before the tsunami pushed matters forward, military-to-military relations between Indonesia and various Western nations were improving. On a visit to Indonesia late last year, Defence Minister Robert Hill said the resumption of full military ties between Australia and Indonesia was proceeding slowly but surely.

Officers from the notorious Kopassus had observed Australian SAS officers in training exercises in Perth, and SAS had in turned been invited to observe exercises in Indonesia. As yet, though, the minister said, there were no plans for joint exercises. "We want to rebuild the defence relationship but we will do it at a pace with which both sides are comfortable," he explained. Indonesia had worked hard to improve respect for human rights within the nation's security forces, Hill added.

Yet beyond a certain point, it is hard to see how much the Indonesian military can improve, when it must find an estimated 70 per cent of its budget from often crooked business dealings. The armed forces have been accused of dealing in drugs, of illegal logging, of racketeering and running protection rackets. Indonesia, struggling with massive debt and endemic poverty, can't afford to pay the soldiers adequately, nor equip them properly, but there is an enormous nationalist fervour which breeds a reluctance to streamline the forces.

And now there is another spectre on the horizon. The armed forces chief, General Endriartono Sutarto, is likely to be replaced soon, and the betting is that army chief General Ryamizard Ryacudu will get his job. Ryacudu has suggested "developed nations" are intent on crippling Indonesia to exploit its natural resources, that anyone who opposed martial law in Aceh was automatically a rebel, and that Indonesia has been infiltrated by hundreds of foreign spies.

[Sian Powell is The Australian's Jakarta correspondent.]