"Offensive" material about West Papua displayed at an Australian Special Forces base has prompted Indonesia's defence chief to cut military cooperation, throwing future joint exercises into doubt.

Key points: An Indonesian instructor took offence to poster displayed at SAS in Perth

An Indonesian instructor took offence to poster displayed at SAS in Perth All cooperation between the Indonesian and Australian military has been suspended

All cooperation between the Indonesian and Australian military has been suspended Future of Australia's defence ties with Indonesia are uncertain

The ABC has confirmed an Indonesian officer complained about the "insulting" training posters at the SAS headquarters in Perth in November last year, prompting Australian Defence leaders to launch furious efforts to try to smooth relations with their counterparts in Jakarta.

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

Indonesian Special Forces group Kopassus trains with the Special Air Service at the unit's Campbell Barracks in Perth.

Major General Wuryanto would not confirm the reason for the suspension, saying it was for technical matters, and that there were "ups and downs in every cooperation between two national forces".

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

Sources familiar with the incident have confirmed the "laminated material" concerned perhaps Indonesia's most sensitive topic — West Papua, which is an Indonesian province that has tried to seek independence from Jakarta.

Defence Minister Marise Payne confirmed the complaints concerned "some teaching materials and remarks" at an Army language training facility in Australia, and that some military cooperation with Indonesia was now on hold.

Senator Payne told the ABC that the concerns were raised in November, though she first addressed the issue of suspended defence cooperation with her Indonesian counterpart this week.

She said cooperation in some areas — such as addressing asylum seeker vessels — continued.

"We have been communicating with our counterparts at the appropriate level to manage this process," she said.

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.

"Indonesia has informed Australia that defence cooperation would be suspended," Senator Payne said in a statement.

"As a result, some interaction between the two Defence organisations has been postponed until the matter is resolved. Cooperation in other areas is continuing."

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".

Defence chief wrote to Indonesia about material

The instructor who was offended was with Indonesian Special Forces group Kopassus (pictured) ( Reuters: Beawiharta Beawiharta )

Sorry, this video has expired Jim Molan: Canberra and Jakarta "unaware" of Indonesian defence chief's decision to cut military cooperation.

The ABC has learned that on November 23 last year, ADF chief Air Chief Marshal Mark Binskin wrote to his Indonesian counterpart about the offending material.

A diplomatic source familiar with the correspondence said the Defence chief's letter reassured the Indonesian military that the offensive material displayed in Perth did not reflect the view of Australia's Defence Force, and was an isolated incident.

Australia's Chief of Army Lieutenant General Angus Campbell also wrote to his Indonesian counterpart on November 24 to reassure him that Australia did not endorse the material.

The Defence Force is yet to respond to questions from the ABC, but senior figures have expressed surprise at the comments from Indonesia's military.

Future of Navy exercises unclear

It is unclear how long the suspension is for or whether the suspension will affect future joint training exercises between Indonesia and Australia.

The Indonesian and Australian navies are due to participate in multinational training exercises in February.

Indonesia and Australia are due to participate in multinational navy training exercises in February. ( ABC News: Nadia Daly )

A spokesman for the Indonesian Navy said he had just found out about the military chief's "statement about the suspension of cooperation with Australia".

"Whether or not we will continue with the joint exercise, I will have to get back to you on that," First Admiral Jonias Mozes Sipasulta said.

"I need to build more details first. Usually we don't suspend cooperation on education and training but now I heard we've suspended all cooperation."

Until this incident the military relationship between the two nations had been improving.

Military cooperation between the two nations was last suspended in 2013 over a phone-tapping scandal.

Documents obtained by the ABC and Guardian Australia revealed that in 2009, Australian intelligence attempted to tap the mobile phone of then-president Susilo Bambang Yudhoyono.