There are many sound reasons why the United States – and Australia – should resist wading back into the moral quagmire which military co-operation with the Indonesian armed forces represents.

Not least must be doubts over whether the resumption of defence ties can blunt support for Islamic extremists inside Indonesia, when these same armed groups – including those linked to the al-Qaeda terrorist network – have been supported by factions within the Indonesian military itself. In these circumstances, a policy reversal would seem to demand a certain compromise of human rights principles, but offer an uncertain strategic outcome.

Both the United States and Australia severed defence ties with Indonesia over the military-led carnage in East Timor in 1999. Australia tentatively resumed training ties earlier this year, specifically excluding Indonesia's notorious special forces. The US Congress is poised to resume military co-operation, arguing that Indonesia is crucial to its anti-terrorism campaign because a struggle is under way between moderate Indonesian democrats and Islamic extremists in the world's most populous Muslim nation.

With a weak central government and corrupt institutions, the vast, poorly policed Indonesian archipelago is, certainly, vulnerable to infiltration by terrorist groups. However, the danger of radical Islam cannot be addressed without understanding the manner in which religious tensions are being manipulated by disgruntled generals and politicians.

Indonesian military officers have ignored or actively supported the extremist Laskar "Jihad" movement, which has provoked bloody sectarian conflicts with minority Christian communities. Such civil strife is intended to destabilise the civilian government in Jakarta, and strengthen the view that a powerful security apparatus is needed.

Radical Islam, itself, has traditionally had little grass roots support in Indonesia. Any intervention by the US military in complex, internal conflicts in Indonesia, however, could inflame nationalist sentiments and strengthen, not undermine, radical Muslim groups.

The US, like Australia, has previously linked the resumption of defence ties to meaningful reforms of the Indonesian military. This is a sound position. No policy change should be implemented before the current trials of Indonesian soldiers responsible for atrocities in East Timor are complete.

Unfortunately, it seems likely the most senior officers will escape punishment. Wider reforms, too, are stalled. At this juncture, the Indonesian military would make a problematic partner in the "war against terrorism" and a mockery of the principles upon which it was so recently shunned.