John Howard has insisted that Australia was “not interested in picking sides” in the conflict in Aceh, but could such a moved be to our detriment and that of the Acehnese people?

Two and a half weeks after the Asian tsunami and the media are finally starting to pay some attention to its implications for the region’s politics – most obviously, the long-running civil war in Aceh.

After all, even with a tragedy of this scope, you eventually run out of new material. Reporters have to either abandon the story or look for spinoffs. And the Aceh question is so far the most interesting spinoff by a long chalk.

Friday’s Australian has a fine story by Stephen Fitzpatrick, who found and spoke to a band of fighters from the Free Aceh Movement, the GAM.

The story in Aceh is fundamentally the same as that in East Timor and West Papua: a people who have never accepted their subjugation by the Javanese empire, and who continue to fight for self-determination despite the hostility of westerners in general and the Australian government in particular.

But the tsunami has changed the dynamics of this story, probably permanently. The genie cannot be put back in the bottle. Now that the attention of the outside world has been focused on Aceh, it will be impossible for the Indonesian military to go back to waging war in secret against the independence movement.

They will try, of course. On January 13, Indonesia announced that it “would bolster its military presence in Aceh to 50,000 troops.” The military’s spokesman insisted that “the fresh soldiers would focus solely on humanitarian operations.” But international pressure is the only thing that can hold Indonesia to that promise.

John Howard insisted that Australia was “not interested in picking sides” in the conflict in Aceh. But of course Australian policy for 40 years has involved taking the side of the Javanese imperialists against their subject nations, by repeatedly insisting that they were all “internal matters” for Indonesia – except for a brief period in East Timor when this policy became unsustainable.

In the case of Aceh, the Indonesian army’s position depends on convincing western governments that they are the bulwarks of pro-western civilisation, while the separatists are Islamic fundamentalists and/or Al-Qaeda-style terrorists. This is the same strategy the Putin government has used with great success in Chechnya, and that Serbia attempted, less successfully, in relation to Kosovo.

But the last few days in Aceh have shown that it is the fundamentalists who are pro-Army and anti-separatist, while it is the GAM that is worried about the influence of the fundamentalists – as these stories from Tuesday, Jan 11 and Wednesday, Jan 12 make clear.

First the head of the Islamic Defender’s Front warned that “Australian assistance in Aceh could herald the start of an East Timor-style intervention designed to secure independence for the troubled northern province.”

He “feared the presence of hundreds of Australian troops in Aceh would corrupt the province’s strict Islamic culture,” and “accused Canberra of using the excuse of humanitarian assistance to support a long-term strategy of undermining Indonesian sovereignty.”

The next day, Indonesia’s most famous Islamic militant, Abu Bakar Bashir, head of the Al-Qaeda-linked Jemaah Islamiah, got into the act as well. His spokesman said that he “regarded the relief operations by Australian and US military personnel as a dangerous development, overshadowing the role of the Indonesian Armed Forces (TNI).”

“It’s dangerous, this idea by Acehnese that US and Australian forces are their guardian angels – more popular than the TNI,” he said.

The Indonesian lobby would like to convince us that the TNI are Australia’s natural allies against terrorism and fundamentalism, but the truth is just the opposite. It is the Islamists and the Indonesian military that are natural allies; the guerillas in the Acehnese mountains are the ones that hope for – and deserve – our support.