David Manne is a refugee advocate who has been a fierce critic of Australia's harsh policies towards asylum-seekers, someone the Howard Government would have dismissed not so long ago as a usual suspect.

So his latest comments are worth noting. Manne is co-ordinator of the Refugee and Immigration Legal Centre in Melbourne and was the senior lawyer representing the 43 West Papuans who came by boat to Australia and have been accepted as refugees, with the exception of one whose case is still being processed.

Manne says: "Their treatment and the due legal process provided by the Australian Government and the Department of Immigration has been fair, reasonable, just and decent, refreshingly so."

Would he extend such high praise to Immigration Minister Amanda Vanstone? Yes, says Manne unhesitatingly: "Credit where it is due and it is due. I think there was a straight bat played on this."

Manne had cause to be apprehensive on behalf of his clients. There are some big issues in play, such as Australian-Indonesian relations, which John Howard has been working hard to repair in the wake of the East Timor crisis of 1999. Despite strenuous denials from the Government and Opposition, the refugee decision feeds Indonesian conspiracy theories that Australia is covertly backing independence in West Papua.

The economic stakes are much higher than in Timor, mainly because of the revenue Jakarta gains from Freeport, the world's largest goldmine.

President Susilo Bambang Yudhoyono rang Howard to offer a guarantee that the Papuans would not be harmed if Australia returned them. Yet apparently neither Howard nor Vanstone intervened in the immigration department assessment of these cases under the Refugee Convention, despite an outcome that found there was a chance the refugees would have suffered serious harm if forced to return.

Moreover, the decision was made quickly, with the applications granted less than two months after they were lodged. That is in contrast to the years it took to process many of the Iraqi and Afghan boatpeople while they were locked away in remote detention camps and even though 90 per cent were ultimately accepted as refugees.

But the starkest comparison is with the more than 1300 people who fled East Timor after the massacre in Santa Cruz cemetery in 1991. So scared were the Keating and Howard governments of offending Indonesia that they refused to process their cases for 10 years, leaving them in limbo in Australia and relying largely on churches and charities for support. Only after East Timor gained independence did the Government grant them permanent residence and then only because of public outrage at attempts to force them to go back. As Manne says, "It was one of the most scandalous misuses of the system in recent times."

Of course, the Government was in a bind over the West Papuans. They had attracted a great deal of publicity and Australia would have been rightly condemned if they were persecuted on their return. Even if the presidential guarantee of their safety is well intentioned, there is no effective civilian control over the Indonesian military, particularly in West Papua.

Abuses of human rights in the province are numerous, serious and becoming more frequent. The US Department of State's recently released report on human rights is more restrained than other studies. But it documents gross violations in West Papua, including murder, assaults, torture, the razing of villages and forced displacements. It notes that indigenous people suffer from widespread discrimination. It says four people were convicted of treason for raising the separatist Morning Star flag and given jail sentences of four to 15 years.

This was the same crime that resulted in one of those Australia has just accepted as a refugee, Herman Wanggai, being jailed for a year. By contrast, the leader of the Kopassus team that assassinated tribal leader Theys Eluay in 2001 received a three-year sentence. Indonesia has restricted the entry of UN and other human rights representatives, as well as academics and journalists.

Indonesia has increased troop numbers in the province. In January, a demonstration turned into a riot after police fired shots into the crowd. Four policemen and a security officer were killed, and at least one protester killed and others injured.

If this sounds like a replay of the years of violence in East Timor that culminated in the carnage and destruction after the independence vote, then that is all the more reason to encourage Indonesia to negotiate the kind of settlement it has reached in Aceh.

The Government's decision on the West Papuans comes in the context of a much improved system of handling asylum applications following the changes forced on Howard by Liberal dissidents led by Petro Georgiou. Children have been released from detention and most of the asylum-seekers who were initially granted temporary protection visas are now allowed to stay permanently.

There is still unfinished business, including the TPVs. These are a reminder of the bad old days, when they were invented as a grudging form of recognition that we were obliged to accept refugees from Iraq and Afghanistan. They turn refugees, including the West Papuans, into second-class citizens, denying them the rights to travel overseas or bring family members to join them in Australia.

Critics argue that the Government's compassion has come too late and only because the political heat has gone out of the boatpeople issue. But sometimes we should suspend cynicism. Credit where credit is due.