Australian Defence Minister Marise Payne rebutted accusations that a secret spy programme had derailed the joint military training with Indonesia. "That is not the case and it is something which we would not countenance, of course," Payne said while speaking to ABC Radio.
"This is a relationship which has been ongoing over many decades in its training activities and co-operation... The investigation requires an examination of materials, requires interviews with the Australians involved and requires an opportunity for the Indonesian officer to comment. These things need to be done appropriately and fairly. They take time but it is close to finalisation," the minister said.
Indonesia said on Wednesday it was suspending military co-operation with Australia. Though Jakarta did not give a specific reason, various theories surfaced, including that Indonesia feared that Australia may recruit its soldiers as spies.
Following Jakarta's decision, Indonesian military TNI's special forces group Kopassus stopped its training sessions with the Australian Special Air Service in Perth. Indonesian newspaper Kompas said a special forces instructor found "laminated material" that allegedly demeaned the 'Pancasila', the country's founding ideology.
"All forms of co-operation with the Australian military, including joint training, have been temporarily withheld. I hope it can be resolved as soon as possible," Army spokesman Maj Gen Wuryanto said.
Indonesia officially said the termination of joint training with Australian forces was due to multiple reasons. However, Indonesian media said the latest spat between the countries came after soldiers in the special forces unit Kopassus said some teaching materials insulting the Indonesian military and flouted the principles in the 'Pancasila' or Five Principles.
The portmanteau word deriving from Sanskrit encapsulates Indonesia's founding principles of One God system, just and civilised humanity, unity, democracy and social justice. Under the 'one god' system all Indonesians are bound to have religious faith as atheism is illegal.
However, Australian media said the lowest point in bilateral relations since the April 2015 execution of two Australian nationals for drug offenses in Indonesia was over Jakarta's fears over an alleged spy programme.
Indonesian General Gatot Nurmantyo had earlier raised concerns that his best soldiers risked being 'recruited' by Australia. "Every time there is a training program â like recently â the best five or 10 students would be sent to Australia. That happened before I was chief so I let that happen," the General had said in late November.
"Once I became chief commander of the national forces, it did not happen again. They will certainly be recruited. They will certainly be recruited," the general said.
The Age also reported that the training material under scrutiny included documents that suggested West Papua was part of Melanesia and should be given independence.
Australia said its armed forces are looking into the serious concerns raised by Indonesia. "Late last year concerns were raised by an Indonesian TNI (Indonesian National Armed Forces) officer about some teaching materials and remarks at an Army language training facility in Australia," Defence Minister Marise Payne said in a statement.
The joint training between Indonesia and Australia has come under stress before as well, notably after accusations that Kopassus was involved in abuses in East Timor in 1999. The two countries' counter terrorism priorities prompted a restart of the joint training following the Bali night club bombing of 2002.