Cartoonists might make light of it, but the view from Jakarta of separatist unrest in Papua is anything but funny. Papua is many times larger than East Timor and Aceh combined. Its complex Melanesian tribal society has a long list of legitimate grievances against Jakarta including a massive transmigration program, the giant Freeport copper and gold mine and Indonesia's failure to fully implement a special autonomy law of 2001.

Papua also has a long and porous border with Papua New Guinea, which is hardly in a position to prevent separatists using its territory as a sanctuary.

Any full blown push for independence is likely to be long and bloody and it won't be limited to bows and arrows. The view from Canberra is just as serious. As in East Timor, it would take very little effort for Jakarta to encourage local militias to harass or kill separatist leaders and their supporters. The number of boat people making the journey to Australia would skyrocket and the local pro-Papua lobby would become hard to ignore. Were this to occur, Australia would be forced to shoulder the burden as it did in East Timor, but multiplied many fold.

At stake for Australia is an important bilateral relationship based on shared concerns such as combating terrorism and stopping people smuggling.

President Susilo Bambang Yudhoyono's decision to review ties with Australia is regrettable given that it is in both countries' interests to work together to ensure stability in our region. While Dr Yudhoyono surely had one eye on his domestic constituency when he branded Australia's decision to grant asylum to 42 Papuans "inappropriate and unrealistic", he must understand Australia will not compromise on the law governing the rights of asylum-seekers.

If Dr Yudhoyono wants to maintain the status quo, he should understand that sovereignty comes with obligations. So far there is little to indicate that policy-makers in Jakarta are looking seriously at the problem of Papua and how to prevent nationalists from getting the upper hand. Years of civil unrest in Aceh and East Timor should be a reminder that a heavy-handed military response is not the answer.

Nor is it productive to perpetuate the myth that Canberra is somehow gunning for Papua's independence. If a butterfly beats its wings in the offices of an NGO, the windstorm does not blow through the Indonesia desk of DFAT. Dialogue that promotes transparency and understanding in Indonesia's treatment of Papua is far better than hiding behind hurt feelings. Dr Yudhoyono must ensure Indonesia does not return to the dark days of the Suharto era when dealing with minorities.

Yet given the underhanded method by which Papua was incorporated into Indonesia in 1969 and how little in common there is between the people of Jayapura and Java, it is hard to imagine Papua remaining a part of Indonesia without more autonomy. Jakarta and Canberra may each have their respective views regarding their fate, but the aspirations of the Papuans will not go away – and will one day have to be dealt with.