Defence Minister Marise Payne has rejected claims Australia has been recruiting members of the Indonesian military to become "agents of influence", as the Turnbull Government races to mend relations amid an immediate suspension of military cooperation between the two countries.

Key points: Fears Australia recruiting "top" Indonesia soldiers are unfounded, Senator Marise Payne says

Fears Australia recruiting "top" Indonesia soldiers are unfounded, Senator Marise Payne says Senator Payne confirmed suspension of defence cooperation, but collaboration in other areas continues

Senator Payne confirmed suspension of defence cooperation, but collaboration in other areas continues No timeframe given for expected resumption of cooperation

An investigation is underway after a member of the Indonesian Special Forces group Kopassus complained in late November about the "insulting" training posters at the Special Air Service headquarters in Perth, concerning the Indonesian province of West Papua.

An Indonesian military spokesman told the ABC cooperation between Indonesia and the Australian Defence Force (ADF) had been suspended, effective immediately.

President Joko Widodo said the issue needed to be clarified at an operational level so the situation did not escalate, and that relations with Australia remained good despite the suspension.

Indonesia's Defence Minister earlier told the Reuters news agency he was not consulted over the move.

Senator Payne said the conclusion of the investigation was "imminent".

Senator Payne told the ABC that fears raised by Indonesia's military chief General Gatot Nurmantyo that Australia was recruiting soldiers were unfounded.

"It is something that we would not countenance, of course," she said.

Senator Payne said the situation was regrettable, but the material which prompted the suspension of defence cooperation had been removed.

"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," she said.

Sorry, this video has expired Jakarta has suspended all military operations with Australia

No timeframe has been provided for an expected resumption of cooperation and Senator Payne could not confirm whether joint exercises between the Australian and Indonesian navies would go ahead next month.

She said some areas of cooperation continued and underlined Australia's position on West Papua, an Indonesian province that has tried to seek independence from Jakarta.

"The issue of West Papua was raised by the Indonesian Defence Minister," she said.

"We of course, in accordance 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."

In a separate statement, the Defence Minister said Australia was committed "to building a strong Defence relationship with Indonesia" and would "work with Indonesia to restore full cooperation as soon as possible".

Indonesian General 'appears to have acted unilaterally'

General Gatot Nurmantyo spoke about soldiers being cultivated as sources or agents of influence during a speech in late November.

Sorry, this video has expired Dr John Blaxland says the suspension of military ties is serious.

During the speech, uncovered by the ABC, he said he suspended the program of sending students to Australia once be became the chief commander of the national forces.

Associate Professor Greg Fealy, from the Australian National University's Bell School of Asia-Pacific Affairs, said the claims were similar to ones made in the past.

He said while the comments themselves were not surprising, the actions that followed were.

"He appears to have acted unilaterally in suspending what is quite an important part of the bilateral military relationship between Australia and Indonesia, without consulting his Defence Minister, nor without having this matter taken to the Cabinet," he said.

"The whole principle of civilian oversight of the military is called into question by the general's behaviour here."