Harold Crouch – Indonesians have reacted with outrage at the Australian decision to grant temporary protection visas to 42 of the 43 Papuans who reached Cape York in an outrigger canoe two months ago.
By granting the visas, Australia is acknowledging the credibility of the Papuans' claim that they fled "from the intimidation of the killing and the persecution inflicted by Indonesian authorities against us".
The withdrawal of the Indonesian ambassador in protest indicates that Australia faces a serious problem in managing its relations with Indonesia. Still, it is premature to suggest that Australia is moving towards the sort of breakdown that occurred during the East Timor crisis of 1999.
Since the loss of East Timor in 1999, Indonesia has been obsessed with the possibility of national disintegration. In fact, there are no serious separatist pressures in most of Indonesia. Armed separatist movements have been active since 1999 in only two provinces – Aceh and Papua – which together make up about 3 per cent of Indonesia's population. In both cases, the mainstream military opposed compromises with rebels and preferred to concentrate on "eliminating" them through military action.
In Aceh, after much bloodshed over many years, a peace agreement that promises to integrate former rebels into a democratic political process, was finally reached last August in Helsinki.
It is important to remember that leading members of the peace camp now occupy top positions in the Indonesian Government. President Susilo Bambang Yudhoyono and Vice President Jusuf Kalla both played important roles in this process long before they attained their present offices, while Foreign Minister Hassan Wirajuda was Indonesia's negotiator in the first round of talks in 2000.
Progress has been much less marked in Papua where the small Free Papua Organisation, with its obsolete weapons, launches occasional isolated attacks but has never constituted a serious military challenge.
Discontent with Jakarta, however, is widespread. Even local government officials in casual conversations often refer to the central government as "Indonesia", as though Papua is not part of Indonesia.
Following the fall of president Suharto in 1998, a non-violent independence movement led by Theys Eluay garnered substantial support until Eluay was murdered by Special Forces soldiers after being invited to a dinner at their base in 2001. Non-violent activists have often been imprisoned for symbolic acts of resistance such as singing the Papuan anthem and raising the Papuan flag.
Among them was the leader of the current batch of refugees, Herman Wanggai, who served a year in prison for this crime. In recent times much unrest in Papua has focused on the exploitation of resources by the giant Freeport gold and copper mine and the failure of the Indonesian Government to implement fully a special autonomy law adopted in 2001.
It is in this context that Indonesian officials are now talking as though Australia's granting of visas to Papuan refugees is tantamount to challenging Indonesian sovereignty over Papua. They claim that Australia "vigorously" rejects applicants for asylum from other countries but rushes to grant asylum to Papuans, evidence, they suggest, that Australia must have some hidden motives (although in fact Australia provides asylum to thousands of non-Papuans from all over the world).
The chief security minister, Admiral Widodo Adisutjipto, spoke of "speculation about the presence of elements in Australia who support the separatist movement in Papua" and the chief of intelligence revealed the "involvement" of unnamed Australian non-government organisations in the clash between students and police near Jayapura a fortnight ago.
Behind these attitudes is the persistent, if usually unstated, belief that Australia somehow plotted East Timor's exit from Indonesia and is now looking for a way to implement a similar scenario for Papua.
Indonesian officials have attempted to assure the recent refugees that they can safely return home. The military commander says the military was not searching for them before their flight and the Government has "guaranteed their security" if they decide to return.
But the problem with guarantees of security is that the past behaviour of the security forces has made it difficult for Papuans to have much confidence in such promises. Although the murderers of Eluay were eventually brought to court in 2003, they seemed proud of their achievement, their sentences were short (their leader, a lieutenant-colonel received three years) and the then army chief of staff, General Ryamizard Ryacudu, hailed them as "national heroes" for their defence of Indonesian sovereignty, an attitude that reflected the sentiments of many military officers. Until Indonesia's military reformers can bring about a transformation of military culture, it will not be easy to convince Papuan dissidents that their rights are likely to be respected.
Australia and Indonesia have experienced regular mini-crises in their relations that usually prompt observers to declare that ties have reached their lowest point since East Timor. Often the substantial issue in such crises – Schapelle Corby, the Bali Nine or Papuan asylum-seekers – are irresolvable. We don't have much choice but to accept that there will be differences in approach.
But that doesn't mean that such differences can't be managed. During the past few years, the multiple strands connecting the two countries have created beneficial bonds at many levels that neither would want to see broken.
Without doubting the genuineness of Indonesian protests on the visa issue, it is likely that Yudhoyono and his advisers are focusing their attention on a more pressing domestic problem. Next month the Indonesian parliament is expected to vote on a law to implement the Aceh peace agreement. The bill is facing strong opposition from nationalist elements in the parliament, the same people who are most vocal on the issue of Papuans gaining refugee status in Australia. Even former presidents Megawati Sukarnoputri and Abdurrahman Wahid are among those who believe the Government is making too many compromises on Aceh.
If the Government upsets the nationalists by soft-pedalling on the Papuan issue, it is not impossible that it could find it harder to pass the Aceh law relatively intact, with the risk that the peace achieved in Helsinki could be threatened.
The Australian Government, with bipartisan support, is right to downplay the present crisis. One lesson of the East Timor experience is that, while maintaining our position, we should avoid statements that stir up public opinion in Indonesia and make it more difficult for Indonesia's leaders to preserve the warm relations that have been achieved in recent years.
[Harold Crouch, a former director of the International Crisis Group's Indonesia project, is an emeritus professor in the research school of Pacific and Asian studies at the Australian National University in Canberra.]