When 43 Papuan separatists washed up on Cape York last January in a 25m outrigger canoe and demanded asylum, they opened up the biggest rift in Australia-Indonesian relations since East Timor – one that has led to the recall of Indonesia's ambassador to Jakarta for "consultations".

The granting on Thursday of temporary protection visas to 42 of the 43 asylum-seekers – some of whom had previously done time in Indonesian jails for hoisting independence flags and committing other crimes of "rebellion" – has infuriated Jakarta. With Immigration Minister Amanda Vanstone's decision to issue the visas comes a tacit acknowledgment by Canberra that these separatists hold legitimate fear of facing persecution were they to be returned to their home country.

And indeed this is almost surely the case: those involved in separatist activities on the resource-rich island province of eastern Indonesia have faced summary beatings and arrests, while the US State Department's human rights assessment of Indonesia speaks of extrajudicial killings, torture and the arbitrary detention of activists.

But while Indonesia's human rights record in Papua may be troubling, and the Department of Immigration and Multicultural Affairs may have rankled Jakarta by granting the visas – Indonesian President Susilo Bambang Yudhoyono even telephoned Prime Minister John Howard to lobby against the decision – this should not be allowed to upset the increasingly close and vital relationship between the two nations.

The situation in Papua today is quite different to that in East Timor years ago. And Indonesians, from Mr Yudhoyono on down, must understand that the decision to grant these 42 visas was administrative, not political (even if this logic is slightly disingenuous), and that Australia has no interest in an independent Papua or the balkanisation of our northern neighbour.

This was underlined earlier this month by Australia's US ambassador, Dennis Richardson, who told a US-Indonesia business lunch, at which Indonesia's US ambassador was present: "Papua is part of the sovereign territory of Indonesia and always has been.

As far as Australia is concerned, Papua is an integral part of Indonesia." We have too many common interests with Indonesia, the world's most populous Muslim nation and a functioning democracy that has lately made great strides against corruption – from illegal fishing to people-smuggling to terrorism – to let the relationship be sidetracked by this one issue. Despite its bluster, Jakarta should get this.

In repairing relations with Jakarta, it will be important for Canberra – and indeed all players – to accept the decision as made in Amanda Vanstone's office and not John Howard's. Of course, the visas would never have been granted without the Prime Minister's approval, but this fact is one that, if quietly ignored, will let all parties save face.

And there is a sense Jakarta is willing to play the game. When the Indonesian Department of Foreign Affairs announced it was summoning the Australian ambassador to Jakarta in for a not-so-friendly chat on Thursday, the statement referred to "the decision by (DIMA)" – not the decision by the Howard Government.

This may seem like hair-splitting semantics, but it's the sort of language that opens the door for a repair of the relationship at the highest levels.

Of course, it would be best if the Papuans and the central Government in Jakarta could sit down in an atmosphere of mutual dialogue in the same way the Acehnese did after the Boxing Day tsunami, carving out a fragile peace.

But until that happens, Indonesia must understand that acknowledging rights abuses and calling for independence are two separate things. The relationship between our two countries is too important to be sidetracked by this one issue.