The prickly relationship between Australia and Indonesia, based on different interpretations of history, has once again found its way into the public spotlight. What sets this latest fracas apart most is its setting – military circles.

Reportedly, teaching materials used to train Indonesian soldiers at Campbell Barracks in Perth, Western Australia, offered sympathy for West Papuan independence, covered the topic of Indonesian war crimes in East Timor, and mocked the nation’s founding principles as “crazy”.

In reaction, Indonesia announced a full suspension of defence cooperation with Australia on Wednesday, only to have former general and senior Cabinet minister Wiranto tell reporters the next day in Jakarta that the suspension only applies to a language programme. For its part, the Australian government announced an investigation into the incident and underscored its stance on the general strength of ties between the two nations.

This Week in Asia contacted the Campbell Barracks on Thursday and later spoke to a defence department spokesperson in Western Australia who could offer no comment, and referred the matter to the capital, Canberra.

Still, the flare up is yet another reminder about the fragility of the friendship between the two nations.

The story gained traction at the highest levels in Indonesia after news outlet Kompas reported on a cable sent by General Gatot Nurmantyo instructing all defence cooperation with Australia be suspended.

Indonesia denies halting all military cooperation with Australia

The instruction materials at issue included “laminated” teaching materials that made fun of Indonesia’s founding five principles of Pancasila – belief in one god, national unity, just and civilised humanity, democracy and social justice. The materials changed the portmanteau word from “five principles” to “panca-gila”, “gila” meaning “crazy”.

Aaron Connelly, an analyst at The Lowy Institute think tank in Sydney, said that it may have been behaviour by the Indonesian general “to limit cooperation and make life difficult for Australia ... The difference here is someone actually reported it this time”.

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Natalie Sambhi, an Indonesian defence specialist at the Perth USAsia Centre at the University of Western Australia, told This Week in Asia that she had not heard of this incident prior to the media reporting it.

“Usually defence has provided a good channel of maintaining communication. It will be harder with some cooperation suspended ... I think this episode has shown the Australian government delivering a clear and consistent message about the value of the relationship with Indonesia, but also being cautious for more information to emerge,” she said.

For Indonesian President Joko “Jokowi” Widodo, it’s “a matter of principle”, as reported by the Jakarta Globe on Thursday. “I think our relations with Australia are still in good condition. Maybe this needs to be implemented at an operational level to avoid heated situations,” he added.

Australian Defence Minister Marise Payne said on Wednesday: “Defence cooperation takes place within the broader context of the Australia-Indonesia relationship, which is in very good shape with extensive cooperation across a wide range of government agencies.”

Areas of cooperation include counterterrorism, and humanitarian efforts, combatting human trafficking and boat arrivals, but even these issues have proven contentious at times.

Though there is hope this latest incident may prove to simply be a short-term bump in the road, it has not always been so. When revelations surfaced in November 2013 that Australia was attempting to tap the phones of President Susilo Bambang Yudhoyono, his wife and other senior officials, Sambhi said diplomatic ties were cut and “it took concerted diplomatic efforts, until August 20, 2014, to establish a code of conduct and ... that occurred under a president far more disposed to Australia”.

Then-Prime Minister Tony Abbott dismissed the story, suggesting that it was normal for nations to “gather information” on one another, a statement Jakarta obviously did not take well.

Australia also lobbied hard to commute the death sentences of two of the Bali Nine – a group of Australians convicted of smuggling heroin. But in 2015 they were executed, 10 years after being convicted.

Australia, under the Gough Whitlam government, said little over Indonesia’s annexation of East Timor, but Australia’s support for Timorese freedom in the lead up to its independence is still sorely felt by Indonesia today.

Indonesia’s hard-won pluralism under threat

Resolution this time has seemingly been swift, but a better understanding, as President Jokowi has said, may be in order for the future. Said Sambhi: “Addressing the pricklier aspect of the relationship such as the history of Australian involvement in East Timor through dialogue in certain circles can start to bridge the gap between Australia’s and Indonesia’s respective interpretations of history. That prickliness over history is a factor in flare-ups related to sovereignty matters like West Papua or boat turnback policies.”

President Widodo was due to visit Sydney and Perth late last year but cancelled the trip thanks to large-scale protests in Jakarta over claims its Christian governor had insulted Islam. The trip, which was for both diplomatic and business purposes, has not yet been rescheduled.

Prime Minister Malcolm Turnbull said at the time: “We agreed the postponement will not affect the need for continued and enhanced cooperation across a range of shared interests and challenges, including the threat of terrorism to our region.”

A resolution is all but certain. However, a better understanding between the nations, who share in a strategically vital relationship, is key to avoiding future rifts.