Greg Sheridan – Is there another boat on the way? This is the question now in Australia-Indonesia relations after the granting of temporary protection visas to 42 West Papuans. The West Papuans came here by boat and claimed they were being persecuted in the troublesome province of Indonesia. This is a big, big, big story.

In response to the Australian grant of protection visas, Jakarta withdrew its ambassador and there were angry denunciations of Australia by Indonesian parliamentarians.

While naturally we do not know the precise motivations of the people who came here by boat, their action is a brilliant stroke in the ongoing political drama of Indonesia, Australia and West Papua.

West Papua could be the new East Timor of Australia-Indonesia relations, only much more troublesome and of much greater long-term significance. The Howard Government understands the stakes very well. It had limited leverage over the decision to grant asylum, which is undertaken after an independent review process by the Department of Immigration and Multicultural Affairs.

Foreign Minister Alexander Downer has done everything in his power to prepare the Indonesians for this decision.

At the end of February Downer went to Jakarta for a day, ostensibly to attend a conference on terrorism. His true purpose was to speak to his Indonesian counterpart, Hassan Wirajuda, about the Papuans. He had four central points to make to Wirajuda.

First, that the Australian Government was steadfastly committed to the policy that West Papua was part of Indonesia and that Indonesia had legitimate and permanent sovereignty over West Papua.

Second, that Australia supported President Susilo Bambang Yudhoyono's efforts to bring about a political settlement in West Papua through a special autonomy package.

Third, that the formal decision on granting temporary protection visas to those involved was not a question of government policy. It would be decided first by immigration department officials acting under set rules that involved international law and treaty obligations.

And fourth, that even if the Papuans were rejected by the department, they would be in Australia for a substantial time because they would inevitably appeal to the Refugee Review Tribunal, and after that to the Federal Court and then the High Court. This whole process could take years.

Downer may not have made the point but such a prolonged process, with the Papuans cast as victims, may well have done much more to polarise Australian opinion against Indonesian rule in West Papua than a decision allowing them to stay.

At one level, the Indonesians have taken this calmly. Wirajuda was polite and friendly in all his conversations with Downer. However, for Indonesia to recall its ambassador is a very serious diplomatic step. It did not take this step all through the turmoil of East Timor.

The official Indonesian statement draws attention to Australia's repeated determination to keep out boatpeople from Middle East nations. These included Iraq when Saddam Hussein was in power and Afghanistan when the Taliban was in power. The Indonesians are affronted that they are seen as not only persecuting their citizens in West Papua but in some sense are registered as worse than these Middle East nations.

But perhaps the most telling sentence in the Indonesian statement was this: "The decision justifies speculations that there are elements in Australia that support separatist movement in Papua."

Many Indonesians see West Papua, and Australia's involvement in it, as another East Timor. For many years Canberra reassured Jakarta that its policy was to recognise Indonesian sovereignty over East Timor, but in the end, from Indonesia's point of view, Australia was crucial in East Timor gaining independence.

Many Indonesians suspect Australia of having a secret, similar game plan for West Papua. The international debate on West Papua will occur mainly in Australia. It will be led mainly by Australian non-government organisations.

It will percolate to the rest of the international community through Australian-based activists. And if an independence referendum is held, it will be because Australia has changed policy. And it will almost inevitably involve Australian soldiers, during the vote or just after. Some elements of this widespread Indonesian perception are clearly wrong.

Canberra never had a conspiracy to make East Timor independent but got caught up in a series of unpredictable events. It was the Indonesians who decided to hold a referendum on the issue and once that decision was made the movement of Australian public opinion was inevitable.

Certainly the Howard Government has absolutely no desire to see an independent West Papua.

Nonetheless, it faces an exquisite dilemma. There are certainly human rights abuses in West Papua and Canberra cannot and should not be blind to that. But in trying to support human rights in West Papua, Canberra wants to give no comfort to the independence movement.

The stakes for Indonesia are enormous. Indonesia has only just got military to military relations re-established with Washington. It is just beginning to attract new foreign investment and register good economic growth. If West Papua becomes an international cause celebre, this could all come under threat.

There are two ways this could happen. A single, gross act of disastrous policy, such as some heavy-handed security operation or massacre, could inflame international opinion, especially in the US Congress.

Alternatively, if a succession of Papuan activists were to row to Australia and repeatedly test our refugee assessment machinery, building on the precedents of these West Papuans, this could become a running sore in the relationship and give the issue a new, heightened international profile. As well as giving Australia a whole new boatpeople problem.

The most encouraging factor is that the Indonesian Government, especially the President, has a lot invested in the relationship with Australia. It won't want to blow it all away over this one incident. Things can probably shortly return to normal. Unless, of course, there are new boats on the horizon.