Members of Indonesia's army have wrapped up a comprehensive joint training exercise in Australia, signalling an improvement in relations between the two militaries since the East Timor crisis two decades ago.

For the past two weeks, Tentara Nasional Indonesia (TNI) soldiers have worked alongside 1st Brigade soldiers in Darwin as part of Exercise Wirra Jaya, which defence says was the first time an Indonesian sub-unit had trained on Australian soil since 1995.

Relations between the two nations collapsed four years later when the Australian-led INTERFET taskforce deployed to East Timor ahead of the territory's push for independence from Indonesia.

Two years ago the Australian Federal Police (AFP) abandoned a war crimes investigation into the TNI's killing of five Australian journalists at Balibo in East Timor in 1975.

Loading

Colonel Steve D'Arcy from the Army's 1st Brigade said the relationship between both armies continued to strengthen.

"We've worked together for a long time and every year, every time we do something like this, that relationship continues to strengthen and build, and it is a very strong relationship and it only gets better," he said.

"Our relationship with Indonesia is vitally important and to underpin that, operations or exercises like this are really important to developing those individual, team and also commander-to-commander relationships," he added.

Since September 11, elements of 5 RAR and the Indonesian Army's 203rd Mechanised Battalion have taken part in partnered combined arms training, urban operations training and a number of professional military education serials.

This morning, Indonesian and Australian soldiers exchanged parting gifts at a farewell parade at Darwin's Robertson Barracks.