Australia expresses regret for offending Indonesia's military

Australia expressed regret on Thursday and promised a thorough investigation of "insulting" teaching material found at a west Australian military base that led to Indonesia suspending defense ties between the often uneasy Asia-Pacific neighbors.

Indonesia confirmed on Wednesday it had suspended military cooperation with Australia in December, a decision that was initially said to have been taken independently by the military.

However, Indonesian President Joko Widodo said on Thursday he had given his permission for the suspension of ties and that his defense minister and military chief had been asked to investigate.

Such military ties cover a range of activities from counterterrorism cooperation to border protection.

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Jakarta and Canberra have had a rocky military relationship in recent years, and Australia stopped joint training exercises with Indonesia's Kopassus special forces after accusations of abuses by the unit in East Timor in 1999, as the territory prepared for independence.

Ties were resumed when cooperation on counterterrorism became imperative after the 2002 bombing of two nightclubs on the resort island of Bali that killed 202 people, including 88 Australians.

Australian Defence Minister Marise Payne said on Thursday an investigation into the offensive materials that were found at Campbell Barracks in the west Australian city of Perth would be concluded "imminently".

"We have indicated our regret that this occurred and that offence was taken. I think that's appropriate when a significant counterpart raises their concerns with you," Payne told reporters in Sydney.

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Australia would present the findings of the report to Indonesia's government and military, Payne said.

Payne refused to reveal the exact nature of the offending material, although Indonesia media have reported that a senior Indonesian military officer training in Australia took offence at a poster questioning Indonesian sovereignty over the western half of the island of Papua.

Media have also reported that the same officer also found documents that ridiculed the founding ideology of Indonesia's National Armed Forces.

Papua, where there is a long-simmering separatist movement, is a politically sensitive issue in Indonesia.

"We of course ... recognize Indonesia's sovereignty and territorial integrity and that is our firm and stated position," Payne said.

She said the offending material had been removed and that all training documents would be "culturally appropriate".

Indonesia most recently suspended military ties with Australia in 2013 over revelations that Australian spies had tapped the mobile telephone of then president Susilo Bambang Yudhoyono.

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Indonesian and Australian officials stressed that the bilateral relationship had not stalled, unlike in 2013.

"I think our relations with Australia remain in a good condition. The problem has to be clarified first at the operational level so the situation will not heat up," Widodo told reporters in Jakarta.

Australia needs Indonesia's help to enforce its controversial immigration policy that includes turning back boats carrying would-be asylum seekers. Payne said there was "no indication" of any change".