Hugh White – In Jakarta, they fear that one of their worst nightmares may be coming to life. For years, Indonesians who know Australia have worried about what happens if the simmering independence movement in West Papua starts to catch the attention and sympathy of the wider Australian community. They fear a repetition of East Timor.

This is the lens through which Indonesia is watching Australia's response to the 43 Papuan asylum seekers now being processed on Christmas Island. A grant of asylum by Australia would mean that Canberra accepts their claims of murderous persecution. And once living in Australia, these people would be free to mount a campaign to promote independence for Papua.

Indonesia's worst fears will have been confirmed by the way politicians from opposite sides of Australian politics have expressed support for the asylum seekers since they have arrived. If this process continues, and public pressure starts to grow in Australia, what would be the chances that any Government in Canberra would stick with the oft-repeated formula about supporting Indonesia's territorial integrity? After East Timor, few in Jakarta are in any doubt. They worry that Australia would dump the bilateral relationship, and become an active, and potentially very effective, advocate on the world stage for Papuan independence.

The Indonesians have a point. It would be tough for any Government in Canberra to put concerns for the bilateral relationship with Jakarta ahead of growing public support for Papuan independence. That would look like going back to the bad old days that both sides of Australian politics have now repudiated, when the foreign policy elites ignored public sentiment and appeased Jakarta over East Timor.

This is why Indonesia's President called John Howard to talk about the issue. This is why the Indonesian ambassador in Canberra, and his Foreign Minister in Jakarta, have both warned that the relationship could be damaged by an Australian decision to grant asylum. And this is why Canberra is treading so carefully.

To understand just how sensitive the issue is in Jakarta, we need to take account of how they see both the Papuan issue, and Australia's role in it.

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, because the nation is defined by its succession to the former Dutch colonial holdings. Indonesia's success in wrestling Papua from the Dutch, who initially withheld it from the new nation, is one of Indonesia's proudest achievements.

Dealing with the independence movement in Papua is one of Indonesia's major challenges. In last year's state of the nation address, President Bambang Susilo Yudhoyono listed it as agenda item one in his program, along with the peace agreement in Aceh. He has been prepared to promote a quite far-reaching special autonomy package for Papua.

But others in Indonesia are less accommodating, and there is significant evidence that elements of the Indonesian military are repeating some of the repressive tactics that have done so much damage elsewhere. Even with good intentions it is hard for Jakarta to send consistent messages to the people of Papua about their future.

However, all sides in Jakarta agree on one thing: they utterly reject independence. And they bitterly resent what they see as outside interference in the issue. As Indonesia's impressive Defence Minister Juwono Sudarsono said over the weekend: "We feel that Indonesia's unity and cohesion would be threatened by foreign intrusion and concern."

And of all foreigners, it is Australia's intrusion that Indonesians fear the most. Since we led the international response in East Timor in 1999, there has been a bizarre but tenacious belief among many Indonesians – even those who know and like Australians – that we have a plan to snatch Papua from Indonesia, just as we did East Timor. Many seem to believe that Australia is deliberately fanning the independence movement.

Some even think we are planning a military operation like Interfet to take over Papua when the time is ripe. These ideas are, of course, completely wrong, but when one explains to Indonesians that Australia has no interest in an independent Papua, they say: "Yes, but that is what you said about East Timor once, too."

Our Government, to be fair, is scrupulous in affirming that Australia does not support Papuan independence. But they also help to fuel the paranoia in Jakarta: more than one minister has described Australia as having "liberated" East Timor, whereas in fact – as the East Timorese Truth and Reconciliation Commission has recently reminded us – for most of 1999 Australia still hoped that East Timor would remain part of Indonesia.

We can hardly complain if some Indonesians misunderstand what we were doing in 1999, if we misrepresent it ourselves.

[Hugh White is a visiting fellow at the Lowy Institute and professor of strategic studies at ANU.]