If there was one thing John Howard wanted as Prime Minister it was to differentiate himself from his Labor predecessor, Paul Keating. Ten years later, Mr Howard finds himself accused of kowtowing to Indonesia over Papua. The Prime Minister is lampooned in political cartoons in much the same way as Mr Keating, who was portrayed as a small, compliant figure at the feet of the former dictator, Soeharto.

It is not what Mr Howard, or Australia, was expecting from the young Indonesian democracy or its first popularly elected President, Susilo Bambang Yudhoyono. Mr Howard has made much of his firm affection for Dr Yudhoyono, and with good reason. Dr Yudhoyono's pro-Western views and reform campaign distinguish him as our most likely good neighbour to date. His election was the best news for the volatile Indonesian-Australian relationship since the fall of the authoritarian Soeharto regime in 1998.

Yet when the head of the Department of Foreign Affairs and Trade, Michael L'Estrange, sits down in Jakarta today to try to ease tensions over Papua, the atmosphere will be decidedly chilly. And Dr Yudhoyono will certainly not be glad-handing the Australian visitor.

Australia has again ended up at Indonesia's feet partly because the Howard Government, and much of the Australian pubic, misjudged Indonesian fervour over Papua. But it is also realpolitik; no matter who is in power in Jakarta, Australia's trade routes run through Indonesian waters, our border protection depends on Indonesian co-operation and our regional counter-terrorism strategy relies heavily on the capacity, and willingness, of Indonesia's security forces to break local terrorist cells and its courts to prosecute.

At the same time, it is reasonable to expect meaningful change in Papua; when Dr Yudhoyono came to power he pushed the grinding misery of separatist conflicts in Aceh and Papua to the top of his agenda. Aceh has since won autonomy and demilitarisation.

But Aceh did not win independence and this is also where the line is drawn for Papua. Australia's perceived undermining of Indonesian sovereignty in Papua – by granting protection visas to 42 Papuans, including independence campaigners – has united Indonesia's political factions. Any personal rapport with Mr Howard aside, rising nationalist sentiment means the Indonesian President has no choice but to stand alongside Australia's most vocal critics.

Contrary to the simplistic view held by many Australians, Papua is not the next East Timor; it is far more complicated. East Timor was of relatively minor economic interest to Jakarta; Papua's Freeport gold and copper mine alone has pumped $US33 billion into the Indonesian economy since 1992, almost 2 per cent of gross domestic product. And Papua is no fledgling nation-in-waiting. While its indigenous Melanesian Christians have no cultural or ethnic affiliation with Indonesia's majority Malay Muslims, they are, themselves, deeply fractured along tribal lines.

The biggest losers in the bilateral row are the long-suffering Papuan people.

While Australia is demonised, the real problem – decades of Indonesian military abuse and the grossly unfair distribution of Papua's natural wealth – can be ignored. Papua's best hope still lies in re-engaging Dr Yudhoyono and his promise of meaningful autonomy, within the Indonesian nation. That is a cause Australia can usefully champion.