Tom Hyland – It's unlikely that Alexander Downer believes what he says about the new row that has erupted between Australia and Indonesia over 42 Papuan asylum seekers.

Despite Indonesian protests over Australia's decision to grant protection visas to the Papuans, Downer says "things will settle down after a short period of time".

Maybe he'll be proved right, on a superficial level at least. After all, it is not in Indonesia's interests to draw too much attention to an Australian decision based on an independent finding that the Papuan boat people have a well-founded fear of persecution.

But Downer is engaged in wishful thinking if he's arguing that the wider issue of West Papua is about to "settle down" or that Australia doesn't risk being dragged into even more perilous diplomatic dilemmas as a result of fundamental flaws in Indonesian rule over its easternmost territories.

Despite, or because of, the good but muddled intentions of Indonesia's new democratic leaders, Jakarta's administration of Papua is at best a mess. At worst, when the security forces have their way, it can be brutal, cynical, corrupt and murderous.

"The core problem for Indonesia in Papua is governance," says Melbourne academic and Papua specialist Richard Chauvel. "How do you rule a place by means other than military ones, with a population that basically doesn't want to be part of Indonesia?"

You rule it with alternating mixtures of persuasion and co-option on the one hand and repression and intimidation on the other, while at the same time applying the old maxim of colonialism – divide and rule.

This is not to say that President Susilo Bambang Yudhoyono is necessarily pulling the levers of both arms. A regional diplomat says Yudhoyono is sincere in his talk of special autonomy, which theoretically will give local people a say in running their own affairs and a share of the revenue from the area's rich natural resources. But Yudhoyono is a long way from West Papua and can't control events there.

In the meantime, Papuan elites are played off against one another. Those who refuse to co-operate with Jakarta are sidelined and ignored. In extreme cases, those who advocate independence are persecuted, tortured, forced into exile, even murdered not on the orders of Yudhoyono in Jakarta, but by military and intelligence agencies who believe they have a sacred duty to uphold the integrity of the nation.

This approach, of course, makes it difficult for Indonesian officials to negotiate with Papuan leaders. "The trouble is, as soon as strong Papuan leaders emerge, the TNI (the Indonesian army) kills them," says one Australian source.

At its simplest, Melanesian Papuans believe their freedom was stolen in a bogus UN-endorsed "Act of Free Choice" in 1969, in which 1022 Papuan "representatives", selected by Indonesian officials, voted for integration with Indonesia after a campaign of intimidation and bribery.

For Indonesia, the issue is one of national identity. The nationalists who founded the modern state laid claim to all of the territory held by their former colonial rulers, the Dutch. When Indonesia gained its independence in 1949, the Netherlands retained control over what is now West Papua, and it became an article of national faith to "recover" it.

Downer's repeated assurances that Australia will always recognise Indonesian sovereignty over West Papua ring hollow – after all, this is what successive

Australian foreign ministers, including Downer, said for more than two decades in relation to East Timor. And even if Australia's words are accepted in Jakarta, Indonesian and Australian officials are sometimes tormented by a similar nightmare.

It goes something like this: an act of violent resistance in West Papua leads to indiscriminate Indonesian reprisals, which are caught on videotape (remember the 1991 Dili massacre?). This in turn prompts outrage in Australia, fanned by pro-Papuan groups. This inflames the latent popular Australian fear of Indonesia (remember the hysteria over Schapelle Corby?), which leads to massive pressure on Canberra to "do something".

Maybe things will "settle down", as Downer hopes. But given the irreconcilable aspirations at work in West Papua, don't expect it to be soon.