Lindsay Murdoch and Tony Wright Jakarta and Jerusalem – Opposition Leader Kim Beazley has urged that Australia's defence forces resume cooperation with Indonesia's military just six months after the country's soldiers were involved in widespread violence and destruction in East Timor.

Speaking during a two-day visit to Jakarta, Mr Beazley said any future cooperation between the two country's armed forces should be part of a more diverse relationship. He said military cooperation "must be supportive of Indonesia's democratic transition".

But Prime Minister John Howard said from Jerusalem yesterday that he believed it was too early to start rebuilding defence ties with Indonesia.

Mr Howard dismissed Mr Beazley's trip to Indonesia as having little impact on the effort to rebuild Australia's relationship with Indonesia. "I don't think it has mattered a great deal either way," he said, adding that he did not wish to politicise the matter.

Mr Beazley referred to remarks by Mr Howard last week in which the Prime Minister said that relations between Indonesia and Australia would never be the same again. "Our relationship will indeed never be the same – for one very positive reason: we are no longer just neighbors in geography but today we are also neighbors in democracy," he said.

Mr Beazley, a former defence minister in the Keating government, pushed the idea of Australian forces undertaking "cooperative endeavors" with Indonesian forces, such as trying to combat the growing problem of piracy at sea.

Relations between the Australian Defence Force and the Indonesian armed forces have been effectively frozen since Australian troops led international forces into East Timor last September to end violence, looting and destruction in the territory by Indonesian troops and their militia allies.

Almost all the senior military commanders blamed for the violence have been promoted and still hold key jobs in the Indonesian armed forces. Indonesian President Abdurrahman Wahid has said that the chief of the armed forces at the time of the violence, General Wiranto, will be pardoned even if an Indonesian court finds him guilty.

Mr Beazley, who presented himself in meetings in Jakarta as the likely next prime minister of Australia, ruled out Australian troops resuming the training of Indonesia's elite Kopassus forces, who are blamed for sponsoring much of the East Timor violence.

But he said: "I think you can see from the things I am saying that we need a mature defence relationship that is based on confidence building."

Mr Beazley said there should be an opportunity to "nut out" problems or concerns that arose with aspects of either Australian or Indonesian security. "This type of talk is important," Mr Beazley said. "When it comes to more cooperative endeavors with forces perse I think we should explore things like the piracy issue, which I think is actually a serious problem."

Mr Beazley criticised Mr Howard for failing to visit Indonesia since Mr Wahid, the country's first democratically elected president, took office last October. "Our national interests ... dictate that we cannot step back from each other just because the going gets tough," Mr Beazley said during a breakfast meeting of the Indonesia-Australian Business Council. "Neither of us can afford to put the other on the shelf for a few years."

Mr Beazley played down problems that have highlighted tensions between Canberra and Jakarta in recent weeks, including the interception by two Indonesian jet fighters of five Australian warplanes flying over eastern Indonesia last week. The Australian planes had proper Indonesian clearances, he said.

He urged Mr Howard to take up Mr Wahid's suggestion of a tripartite commission to solve problems in the region between East Timor, Indonesia and Australia. Mr Wahid told The Age last weekend that he hoped to visit Canberra, Melbourne and Darwin in late July or August, the first visit by an Indonesian president since 1975.

Mr Howard said Australia and Indonesia had to approach their relationship with goodwill and with an eye to the future. But it had to be recognised that the future would be influenced by the past. "I think you just take one thing at a time," he said. "The relationship has gone through strain, that's understood. It is recovering, it is repairing, it is rebuilding."