Ever since John Howard was elected prime minister in March 1996, Australia's relations with its powerful neighbour, Indonesia, have been tempestuous. But today, as a result of the Bali bombing last October and the Marriott Hotel bombing in Jakarta on August 5, the Howard government is moving closer to Indonesia to combat the growing terrorist threat in the Asia-Pacific region. The question is: is this just a temporary alliance of convenience or is Mr Howard seeking to build a genuine long-term friendship? Based on his record so far, a deeper understanding between the two nations still seems a distant prospect. Even in dealing with the immediate crisis, Mr Howard is jeopardising the policy bipartisanship that is critical to any serious re-engagement. This week, Mr Howard announced that Australia was stepping up its co-operation by restoring relations with the Indonesian armed forces - relations that Australia broke off in 1999 in protest against alleged atrocities by the Indonesian military during the East Timor independence referendum. This renewed engagement involves Australian armed forces working closely alongside the Indonesian special forces group, Kopassus. For Mr Howard's political opponents, this is unthinkable. The opposition Labor Party says Kopassus is guilty of human rights abuses throughout Indonesia, and particularly in Aceh, West Papua and East Timor. It also appears to have links to the terrorist organisation Laskar Jihad. When Mr Howard came to office, he wasted little time in ripping up the security agreement that his predecessor Paul Keating had signed with then president Suharto of Indonesia. Indonesia's economic and political turmoil of 1997-98 led Mr Howard's government to assume that Australia could pay less heed to its northern neighbour. In 1999, Australia backed the East Timorese independence push, a move that earned it a great deal of enmity among Indonesians. In fact, when the Australian-led international force arrived in East Timor in September 1999, Indonesia's president Abdurrahman Wahid cried that Australia was 'p***ing in our face'. Just as it seemed the East Timor issue was finally behind the two nations, along came the Bali bombing tragedy in which 88 Australians lost their lives, further exacerbating difficulties. For many Australians, Indonesia was now a nation to be feared. This sentiment allowed Mr Howard an easier time than he otherwise might have had with Indonesia's President Megawati Sukarnoputri in committing Australia to the US-led 'coalition of the willing' in Iraq. Acting outside the auspices of the UN, the war lacked legitimacy in Indonesia's view. Ms Megawati rightly feared that Australia's commitment to the war would make her attempts to curtail Islamic extremism more problematic. In fairness to Mr Howard, Australia reacted swiftly after the Marriott bombing to offer police assistance. The level of co-operation between both countries' intelligence and policing networks in tracking down operatives of the shadowy terrorist outfit, Jemaah Islamiah, has been first rate. But in a sense, this merely proves the point that one of the most important relationships of the Asia-Pacific region is based simply on a mutual aim these days - the eradication of terrorism. The reality is that because of the events and attitudes taken to key issues in the past seven years, relations between Australia and Indonesia remain difficult, despite Mr Howard's recent efforts. Many Indonesians still see Australia as a threat to their country's future stability. They see a 'hidden agenda' of fragmentation of the archipelago that makes up their fragile country. Mr Howard must work assiduously at repairing relations, beyond the issue of co-operation on terrorism. Much greater attention has to be paid to assisting Indonesia to become a transparent, vibrant economy so that economic relations between Australian and Indonesian companies increase substantially. Australia and Indonesia are odd bedfellows - one a stable, prosperous democracy and the other a turbulent, emerging nation. But it is for that very reason that they need each other. For Australia, there is the nightmare possibility that Indonesia might break up into a myriad of small statelets. And for Indonesia, Australia represents a friend who can provide considerable assistance and support as it makes its painful transition to a liberal capitalist democracy. Greg Barns is a freelance writer based in Hobart, Australia