Indonesia appears to have backed down over its suspension of all military cooperation with Australia.

Top cabinet minister Wiranto has issued a statement saying the suspension will only apply to language classes at Special Forces facilities.

It is a reversal from comments made over the past 24 hours and an apparent intervention from the Indonesian Government over the head of military chief Gatot Nurmantyo.

General Gatot is an outspoken critic of Australia who raised concerns about attempts to "recruit" young Indonesian soldiers as intelligence sources.

Defence Minister Marise Payne rejected those claims as unfounded and "something we would not countenance".

Sorry, this video has expired Evan Laksmana, a researcher at the Centre for Strategic and International Studies in Jakarta, says 'everything remains on solid footing'.

Earlier Indonesia's President Joko Widodo said relations with Australia remain in a good condition.

Military ties between the countries were cut after an Indonesian officer complained about "insulting" training posters at the Special Air Service's Campbell Barracks in Perth.

Indonesian Special Forces group Kopassus trains with the SAS at the base.

The complaint, in November last year, prompted Australian Defence leaders to launch furious efforts to try to smooth relations with their counterparts in Jakarta.

Sources familiar with the incident 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.

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

Senator Payne confirmed the complaints concerned "some teaching materials and remarks" at an Army language training facility.

She said the material had been removed.

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.

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