David Costello – If our leaders were to have a collective brain meltdown and press Jakarta over Papua, the regional fallout would be dramatic

At times, the politicians acting in this nation's interest can take it a long way from our core values. This sums up Australia's position not to seriously challenge Indonesia over its appalling treatment of indigenous Melanesians in Papua province.

There is no doubt that crimes against humanity are being perpetrated on our doorstep. Some believe the policies the Indonesian state is pursuing, through its armed forces (TNI) and police, amount to genocide.

A 2003 Yale Law School paper found the evidence "suggests that the Indonesian Government has committed proscribed acts with the intent to destroy the West Papuans... in violation of the 1948 Convention on the Prevention and Punishment of Genocide".

Jakarta took control of what was the Dutch colony of West New Guinea in 1963 and legitimised the seizure in the 1969 Act of Free Choice, in which Papuan representatives were forced at gunpoint to join Indonesia. Since then, the military and police have acted with impunity against the local population.

Reports compiled by the US State Department, the University of Sydney's Centre for Peace and Conflict Studies, Amnesty International and Papuan rights group Els-Ham have documented arbitrary killings, rape and torture as well as forced labour and relocation.

The Yale study claimed that Indonesian authorities destroyed the property and crops of indigenous people and excluded them from upper levels of government, business and education.

Els-Ham says the documented death toll is more than 100,000 but many observers say it is higher.

No one should be surprised at this catalogue of horror. It is a common pattern in "military operations" areas at the mercy of the TNI and its militia groups.

A recent UN-sanctioned report found up to 180,000 East Timorese died as a result of the Indonesian occupation and that the military used rape and starvation as weapons. Papuan separatists took heart from the events of 1999 when East Timor chose independence in a process started by Australian diplomacy.

But the violence unleashed by the TNI and the subsequent intervention by an Australian-led UN force has left deep scars in Canberra and Jakarta. Sections of Indonesia's elite worry Australia is trying to break up their country and secretly supports Papuan independence.

That is why the Howard Government and Labor Opposition preface remarks on the area by pledging support for the territorial integrity of Indonesia.

They say Jakarta should crack down on military excesses and follow up on the 2001 special autonomy package – even though autonomy is a sham and undermined by Jakarta's unconstitutional move to split the province. But the message from Canberra is that Papuans can forget about self-determination – or any independent investigation of human rights.

This, the major parties believe, is not in Australia's interest. And they are correct. If our leaders were to have a collective brain meltdown and seriously press Jakarta over Papua, the regional fallout would be dramatic.

Relations with President Susilo Bambang Yudhoyono and his government would be frozen and a bilateral security treaty, to be signed this year, aborted.

Other Asian countries – including China – would accuse Australia of lecturing and interfering in a neighbour's internal affairs and our participation in meetings such as the Asia-Europe Summit would be at risk.

Washington would not be impressed given that both the US and Australia are resuming links with the TNI with the aim of fighting Islamist terror groups.

Indonesia views the acquisition of the province as one of its key achievements and has vowed never to let it go. It needs the wealth from projects such as the massive Freeport McMoRan gold and copper mine at Grasberg.

If pushed to the wall by foreign intervention, TNI would take a terrible revenge and create a refugee crisis which would destabilise Papua New Guinea.

But for all Australia's caution, the Papua question is erupting again thanks to the 43 asylum seekers who arrived on Cape York in January and are now on Christmas Island. Queensland lobbyists close to the refugees and their leader Herman Wainggai expect the group will get bridging visas allowing them to stay while their cases are assessed.

Indonesia, which has asked for the return of the asylum seekers, would view such action as an acceptance of their claims of persecution. It would also fear the Papuans would use Australia as a base to further their cause. This concern is well-founded.

Until now, Papua has been an issue for the minor parties, with Democrat Senator Natasha Stott Despoja and Green senators Bob Brown and Kerry Nettle expressing concern. But after visiting Christmas Island, Queensland National Party Senator Barnaby Joyce said the Papuans' claims of religious and ethnic persecution should be assessed.

Watching all this are pressure groups, including the Australia West Papua Association. Jason McCloud, a Brisbane-based AWPA spokesman, says Australia should investigate reports of atrocities and support an independent review by the UN Commission on Human Rights.

It should also support observer status for the province at the Pacific Islands Forum. He says the Federal Government should acknowledge Australia's role in Papuan history, particularly its support for the flawed Act of Free Choice.

None of this is going to become mainstream party policy any time soon. But there is a price to pay in the world arena for equivocating when civilians are being slaughtered and starved.

Australia is likely to be judged adversely when the definitive history of this mess is written.

[David Costello is The Courier-Mail's foreign editor.]