In March 2015, when he was army chief of staff, General Gatot said that efforts for East Timor to secede from Indonesia were a proxy war on the part of Australia to secure the oil field in the Timor Gap. (A proxy war is a conflict between two powers in which neither engages the other directly.)

Hints of the lead-up to Indonesia's dramatic decision to suspend military ties with Australia can be found in General Gatot's public lectures over the past two months, posted on YouTube.

He said he pulled a special forces officer from Indonesia, who was teaching at an army base in Perth, after the officer was offended by a homework assignment that said Papua should have independence because it was part of Melanesia.

"Their [Australian] commander apologised to me," General Gatot said. His remarks were greeted with applause.

He was also suspicious of the circulation of US marines through Darwin, now under way for two years, pointing out that it was close to Papua and Indonesia's giant Masela gas block.

And he said he had put a stop to Australia recruiting Indonesia's top-ranked army officers.

But his unilateral decision to halt military ties with Australia (a presidential spokesman said the decision had been not made by President Joko Widodo) caught many off guard.

Even Indonesia's Defence Minister Ryamizard Ryacudu, also a hardline ex-general, who reportedly said last year that communists killed in the 1960s purge "deserved to die", seemed at pains to smooth over the latest diplomatic rift.

He stressed the relationship with Australia was "fine" and pointed out that the Australian lieutenant who had caused the offence had already been reprimanded.

"Don't let insignificant rats disrupt the relationship between countries. That's not good," he said.

There is understood to be a turf war within government circles, given that decisions on breaking off military co-operation would normally be the purview of the defence or foreign affairs minister.

Australia's Defence Minister Marise Payne was also caught on the hop, despite the suspension coming into effect last month, taking hours to issue a statement on Wednesday.

"Gatot jumped the gun. It was supposed to be dealt with quietly," a source told Fairfax Media.

"Gatot has an ambition of becoming president or vice-president," the source said. "And at the same time a lot of people in the military are unhappy with him. This is a good way for him to burnish his nationalism credentials."

Security expert Damien Kingsbury, a professor of international politics at Deakin University, said that, while General Gatot had a history of hostility towards Australia's strategic position, the fact he had unilaterally made the decision to suspend ties without reference to the President was "pretty extraordinary" in bilateral relations.

"It's very strange stuff," Dr Kingsbury said.

"He will have known exactly what the implications of this are in terms of its impact on the bilateral relationship."

Dr Kingsbury said the training materials used at the Perth base were not new and Kopassus special forces officers rotate through training on a regular basis, so presumably many would have seen these materials previously.

"So this raises a question of what Gatot is actually on about - whether it's really about a particular offence being caused or whether there is some other game being played."

The associate editor of The Diplomat, a current affairs magazine for the Asia-Pacific, Prahanth Parameswaran, said Australian officials were surprised the concerns over the allegedly offensive material had been made public, given both sides had committed to investigating and resolving it.

"Gatot has a deeply held and well-known suspicion of foreign powers, and Australia in particular," he said.

"My own take is that, given his views, he saw an opportunity with this incident to play up the challenges in a relationship he is already deeply suspicious of."

President Jokowi, as he is popularly known, is yet to comment on the latest diplomatic spat to beleaguer the bilateral relationship.

However, he is struggling to deal with the fallout from incendiary allegations that Jakarta's Christian governor insulted Islam, which has sparked colossal rallies in the streets of the capital, and the last thing the President would want to have to deal with now is a tiff with Australia.

Many insiders believe it is all a storm in a teacup.

It is highly likely the storm will blow over – especially if Australia makes some sort of statement of regret – and Australia and Indonesia's relationship, always tempestuous, will quickly return to an even keel.

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