Indonesia is an early test for of the new Australian government's foreign policy. The Australian media largely hailed Abbott’s first foreign visit to Jakarta as a success. The trip focused on trade and cooperation on people smuggling. Instead of any public discussion of human rights concerns in Indonesia, Abbott did his utmost to avoid stepping on any Indonesian toes – which is regarded as success in some quarters of the Australian government.

But Abbott was able to dodge Indonesia’s human rights problems only temporarily. On 6 October, three Papuans crashed the Asia Pacific Economic Cooperation (APEC) Summit party by scaling the Australian Consulate’s fence in Bali and presenting a letter urging APEC leaders to pressure the Indonesian government to open Papua to foreign media and to free Papuan political prisoners.

Abbott’s response to this desperate act by three Papuans was immediate condemnation, rather than any attempt at understanding the concerns the Papuans were raising. Abbott decried “people seeking to grandstand against Indonesia; please don’t look to do it in Australia. You are not welcome.” Abbott also went out of his way to reaffirm “Australia’s absolute respect for the territorial integrity of Indonesia” saying “while I acknowledge the right of people to free expression, I acknowledge the right of people to fair treatment under the law, I should also make the point that the people of West Papua are much better off as part of a strong, dynamic and increasingly prosperous Indonesia.”

The acknowledgment of rights was important, but Abbott’s reference to territorial integrity said more about his politics than about the Papuans. In fact, the Papuans demonstrating at the consulate were not armed, were not separatist supporters, and were not even advocating Papua’s independence. Nor were they seeking asylum in Australia. They were simply making a plea for foreign journalists to be able to visit Papua, and for the release of Papuans imprisoned for nonviolent activities such as raising flags or making controversial speeches. Abbott demonstrated an unnerving indifference to the issues by appearing to conflate exposure of Indonesian human rights violations with separatism. This is precisely the mistake Indonesia keeps making, and, to say the least, it is not helping ease tensions in Papua.

There is a large military presence in the region facing the Free Papua Movement (Organisasi Papua Merdeka, OPM), a small separatist armed group active since the 1960s. Government security forces deployed to Papua have frequently been implicated in abuses including excessive use of force against peaceful demonstrators, arbitrary arrest and detention, torture, extrajudicial killings and enforced disappearances. Those who criticise the authorities or investigate human rights abuses are often subjected to surveillance, harassment, and are prone to being labelled separatists.

Two years ago, Human Rights Watch disclosed secret Indonesian military documents that showed how the focus of Indonesian military operations in Papua goes far beyond the OPM rebels and includes surveillance of a broad swathe of Papuan political, traditional, and religious leaders and civil society groups. It is convenient for the Indonesian military to link human rights advocacy and separatism as it enables them to arrest and detain peaceful activists. But the Australian government should know better than to simply repeat such assertions. Doing so puts Papuan activists even further at risk.

Rather than simply seeking to pander to the Indonesian government, Abbott should examine the merits of the arguments raised by the Papuans. Thousands of foreign journalists attended the APEC summit, yet a decades-old restriction effectively prohibits them from visiting this troubled province. On 9 October, the governor of Papua, Lukas Enembe, claimed that the province was now open to journalists and human rights monitors. While this change of heart is welcome, the central government in Jakarta has said that permission is still required from the department of foreign affairs.

The relationship between Australia and Indonesia is complex, but both countries are democracies and democracies should uphold the right to peaceful expression. Abbott claims that ''the situation in West Papua is getting better, not worse.” If it is better, then why doesn’t Jakarta lift the restriction on foreign journalists and free those who are imprisoned for peacefully expressing their views.

Australia needs to get the message to Indonesia that "maintaining strong ties" means ending human rights abuses in Papua.

• This article was commissioned after a suggestion from Pilgrim85