Indonesian President Joko Widodo said on Thursday relations with Australia remained good despite the Indonesian military announcing a day earlier that all military co-operation had been suspended.
"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.
The president's comments come after the Indonesian military suspended ties with their Australian counterparts for "technical reasons" after offensive material was found by an Indonesian officer at a training base in Perth.
According to Indonesia's Military Chief Gatot Nurmantyo the materials not only referenced West Papua, but also East Timor.
"The curriculum and lessons, have always been the same. It is hurting (our feelings), I don't want to elaborate further as the offending teaching materials have been in place for a long time," he told reporters.
"The materials include content about Timor Leste, saying that 'Papua needs to be independent', and mock Pancasila as 'Pancagila'."
Working the Bahasa word for crazy, 'gila', into the reference to the founding principles of 'pancasila', which include belief in god, the unity of Indonesia, social justice and democracy.
"And all the five articles (of Pancasila) are incorrect, so I have withdrawn the teachers and stopped the programme for now," he said.
The suspension of cooperation took effect in a December 29 telegram sent Mr Nurmantyo.
"Marshal Binskin is my good friend and he has sent a letter of apology to me. In the letter he also says that the curriculum will be amended, and thirdly they (Australia) will conduct an investigation. Lastly, they will send the Australian army chief to apologise to the Indonesian army chief and me," he said.
"We have stopped the programme and bilateral talks will continue until the investigation is done."
Army investigating
On Thursday, Ms Payne said the Australian military is investigating the training materials and working to restore the relationship with Indonesia.
"The issue of West Papua was raised by the Indonesian Defence Minister, yes. I think he indicated that in his post-meeting comments," she told reporters.
"We of course, in accord with the Lombok Treaty, which is the treaty between Australia and Indonesia, recognise Indonesia's sovereignty and territorial integrity and that is our firm and stated position."
Indonesia last suspended military ties with Australia in 2013 over revelations that Australian spies had tapped the mobile telephone of then President Susilo Bambang Yudhoyono.
In 1999, Australia stopped joint training exercises with Indonesia's Kopassus special forces after accusations of abuses by the unit in East Timor, as the territory prepared for its independence three years later.
Jakarta and Canberra resumed military ties, saying co-operation on counterterrorism became imperative after the 2002 bombing of two nightclubs on the resort island of Bali that killed 202 people, including 88 Australians.
With ties gradually warming, the first joint training exercise on Australian soil since 1995 was staged in the northern city of Darwin in September last year.
Unrest in Jakarta forced Widodo to postpone a trip to Australia planned for November that had aimed to discuss defence ties, among other subjects.
