The Australian Army is investigating offensive "training materials and remarks" that caused Indonesia to suspend all military co-operation with Australia.
The ABC confirmed an Indonesian officer complained about offensive material pertaining to West Papua at the Special Air Services base in Perth.
Commission I Bobby Adhityo Rizaldi told Kompas, an Indonesian newspaper, that other material included “a laminated paper” that insulted Indonesia’s national philosophy ‘Pancasila’, which is based on five principles: the belief in one God, unity of Indonesia, a just and civilised humanity, democracy and social justice.
Indonesia temporarily suspended all military co-operation between the two countries on December 29 after a member of the Indonesian Special Forces, also known as Kopassus, saw the offensive training material at the Special Air Service base.
Kompas reported the material ridiculed the Indonesian military and that the Indonesian army had sent a letter to Chief of the Australian Defence Force, Air Chief Marshal Mark Binskin, on December 9 about discontinuing the military ties.
A telegram was then sent on December 29 to Air Chief Marshal Binskin calling for the temporary suspension of military co-operation between the ADF and Indonesian National Armed Forces.
"All forms of co-operation have been suspended," Indonesian military spokesman Major General Wuryanto told AAP on Wednesday.
He said a broad range of activities will be affected.
"There are technical matters that need to be discussed," Wuryanto said.
“[The co-operation], this termination is temporary," Wuryanto told another Indonesian media outlet Koran Sindo.
"Only temporary, it’s not a total termination of co-operation between Indonesia and Australia.
"The reason for the cessation is only a technical problem. The usual bilateral co-operation of the armed forces is no more or no less. It’s only that affairs need to be refined, just that.”
Defence Minister Senator Marise Payne told reporters on Thursday the Army was concluding an investigation into the teaching materials.
“The concerns were raised through TNI (Indonesian National Armed Forces) and then back to the Australian military at the end of November and then the beginning of December. The chief of the Indonesian military wrote to the Chief Defence Force on December 9," she said.
“The Chief of Army here in Australia, Lieutenant General Angus Campbell instituted an inquiry that is under way.”
Ms Payne said she took the relationship with Indonesia very seriously and "to do otherwise would be inappropriate".
"Certainly 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, no matter who it is," she said.
"We obviously work very broadly, regionally and internationally, and we should endeavour to ensure that the material we use is culturally appropriate, is to the point not gratuitous, and I am sure that those are matters which will be taken into account in the preparation of training material into the future, and in fact I will ensure that that is the case."
She reassured Indonesia that reinforcing the Australian-Indonesian military relationship and the relationship more broadly would be a top priority.
Kompas quoted the director of the Institute for Defence, Security and Peace Studies in Indonesia, Mufti Makarim, saying it was wrong of the Australian military to enter into Indonesian politics.
"The negative discussion about Indonesian politics in the forum of military exchange education between Indonesia and Australia is surely offensive in regards to the mutual respect between the Indonesian and Australian military," he told Kompas.
"Therefore it is appropriate for Indonesia and Australian co-operation to be temporarily suspended and for the Indonesian defence ministry to officially object."
Defence Minister Ryamizard Ryacudu told local media outlet Tribunn News that the incident involved only one Australian lieutenant who had been "reprimanded, already convicted".
Senator Payne said she and Indonesian Defence Minister Ryamizard "had discussions about the issues that are important to both of our defence organisations and our future areas of co-operation".
The government's , released in 2016, said Australia was committed to deepening the "defence partnership with Indonesia through: navy, army and air force co-operation; expanding our comprehensive pattern of training, exercises, and operations; more frequent policy and planning dialogue; and intelligence exchanges".
Relations between Indonesia and Australia have been frosty in recent years with revelations in 2013 Australia tapped the phone of former Indonesian president Susilo Bambang Yudhoyono as well as those of many people close to him, including his wife.
Military co-operation was suspended at that time as well and Indonesia's ambassador to Australia was recalled.
- with AAP