Crikey reporter Jane Nethercote writes:

Not since East Timor’s battle for independence in 1999 has Australia’s relationship with Indonesia been so strained. The decision by Australia to grant refugee status for 42 of the 43 West Papuans who landed on Cape York two months ago has certainly put the cat among the pigeons.

As Harold Crouch points out in The Oz today, by granting the temporary visas, Australia has basically acknowledged the credibility of the Papuans’ claim that they fled “from the intimidation of the killing and the persecution inflicted by Indonesian authorities against us”. Indonesia has reacted strongly, recalling its ambassador to Australia, Mohammad Hamzah Thayeb, in protest.

Given the history of Australian interference, there is a sense in Indonesia that “certain Australian human-rights groups are now rubbing their hands and thinking they can help to accomplish independence for Papua as well”, writes John McBeth in Asia Times

And therein lies a paradox, Richard Chauvel, Victoria University, tells Crikey. “Australia has a vital interest in assisting Indonesia to resolve the conflict in Papua.” And yet, in some ways, Australia is in the most difficult position to play a role because of the suspicions of Indonesia’s rulers, suspicions that can be traced “directly back to Australia’s role in the international intervention in East Timor”. Foreign Minister Alexander Downer may have visited Jakarta in February to reassure Indonesia that Australia acknowledges its sovereignty over West Papua but the government has made similar noises before.

To understand just how sensitive the issue is in Jakarta, we need to take account of how they see the Papuan issue, wrote Hugh White in The Ageback in February. “Unlike East Timor, Papua was part of the old Dutch East Indies. That makes it central to Indonesia’s image of itself as a nation … Indonesia’s success in wrestling Papua from the Dutch, who initially withheld it from the new nation, is one of Indonesia’s proudest achievements.”

For Indonesia, the situation is complicated and confused, says Chauvel. President Susilo Bambang Yudhoyono may have made public commitments to resolve the issue of West Papua on the basis of the Special Autonomy Law (2001) – most notably in his Independence Day speech. However, some of his government’s recent decisions have made a peaceful resolution more difficult. The president also inherited a serious “policy mess” that stems from Megawati Sukarnoputri’s time in office.

Under Megawati, West Papua was divided into provinces (which resulted in the creation of West Irian Jaya) – ostensibly to make the region easier to manage for Jakarta’s central government. Of course, the division of West Papua has “increased competition among the Papuan elite for positions and control of resources”, remarks Chauvel. And this increased competition within West Papua has helped undermine the movement for independence.

Meanwhile, in what captures the “essence of confusion” over West Papua, says Chauvel, Indonesia’s constitutional court ruled in November 2004 that dividing West Papua was unconstitutional. However, because the province of West Irian Jaya now existed on paper, the court also deemed that “it should be allowed to continue to exist”.

The uncertainties surrounding Jakarta’s policies in Papua have “become a factor in the political instability in the province”, says Chauvel. “Papuans’ confidence in Jakarta’s intentions is at a low point.” The brutal killing of five members of the security forces in the Abepura riots “reflect something of the depth of feeling among Papuans, their desperation and degree of alienation from Indonesia”.