It is turning out to be a storm in a smaller-than-usual teacup, but the latest spat between Jakarta and Canberra over what was perceived to be insulting content in military training materials underlines once again the sensitivities surrounding Indonesia’s often brutal past.

It also speaks to the current state of Jakarta’s domestic politics, with government sources revealing that President Joko Widodo didn’t know armed forces chief General Gatot Nurmantyo had suspended all military cooperation with Australia over the issue.

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Indeed, the sources say he only woke up to what was happening when his close adviser, chief maritime minister and retired special forces general Luhut Panjaitan, received a call last month from an Australian friend asking what more could be done beyond an apology and an investigation.

As the episode broke in the media this week, political coordinating minister Wiranto, a one-time military commander himself, issued a hasty statement saying only language classes had been suspended, not the entire military relationship.

Widodo also sought to play down the fallout, saying relations remained in good shape. So did normally hard-nosed Defence Minister Ryamizard Ryacudu in a January 5 phone conversation with his Australian counterpart, Marise Payne. Payne has said the Australian military must produce “culturally appropriate” training material, which apparently means avoiding any reference to East Timor and Papua where Indonesia has a checkered past.

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The original complaint came from a special forces (Kopassus) language instructor and went up the chain of command to Nurmantyo, an ultra-nationalist with ambitions to run in the 2019 presidential elections.

The armed forces chief is already in Widodo’s bad books for his alleged links with some of the Muslim groups that took part in the recent mass demonstrations against Jakarta Governor Basuki Purnama, who is currently on trial for blasphemy. The protests have rattled Widodo because at one point it appeared they were also directed at weakening him now Indonesia is only two years out from its next presidential election when he is expected to seek a second term.

Nurmantyo has often caused a stir with his wild conspiracy theories, expressed in public speeches and in social media, about how foreigners are engaged in a proxy war to undermine and take over Indonesia.

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Last November, he claimed in a filmed lecture that Australia was trying to recruit young Indonesian officers, undergoing advanced training at various bases across the country, to be either spies or agents of influence.

Conservative elements in the Indonesian Armed Forces have always been suspicious of foreign-trained officers, seeing them as being too favourably disposed towards Western views and attitudes.

Nurmantyo’s predecessor, General Moeldoko, had similar presidential ambitions, but he quickly disappeared after retiring in July 2015. Observers believe the same future awaits Nurmantyo, who is unlikely to find a political party to support him.

What offended the complainant, a Kopassus lieutenant, was the use of what he considered to be a derogatory Wikipedia biography of the late Sarwo Edhie Wibowo, former president Susilo Bambang Yudhoyono’s father-in-law.

The legendary special forces general, whose own son also later commanded the elite regiment, led the purge against the Communist Party of Indonesia in the mid-1960s which claimed the lives of an estimated 500,000 people. He also oversaw the so-called Act of Free Choice, a United Nations-sanctioned referendum – albeit involving only 1,025 Papuan leaders – under which the former Dutch-controlled territory reverted to Indonesian rule in 1969.

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Suspicious of the popular Wibowo as a potential rival for power, Suharto shuffled him off as ambassador to South Korea in 1973. He served there for five years, before returning to fill a variety of backwater posts until his death in 1989 at the age of 64.

The Wibowo biography was not the only source of the lieutenant’s wrath. He was also upset over a poster on a wall at the Australian Special Air Service’s Perth headquarters, which ridiculed Pancasila, the ideology that defines Indonesia as a secular state. The offending poster instead referred to it as Pancagila, the last five letters making the Indonesian word for ‘crazy’, and replaced the five principles of Pancasila with snide references to corruption.

Pancasila made up a big chunk of military instruction during the 32-year rule of President Suharto, something that always bemused foreign officers attending courses at Indonesia’s Army Command and Staff School. One of those officers has a much different view now. “What I saw only partially then, but understood later, was without Pancasila, Indonesia will revert to religion or ethnicity and that means a civil war worse than Aleppo [Syria],” he says.

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Pancasila is nowhere near as prominent in Indonesian education as it once was, but Widodo and other political and moderate religious leaders want to change that as they come under mounting pressure from hard-line Muslim groups seeking to turn the country into a Sharia state.

It is ironic then that Pancasila has more relevance in unifying today’s democratic Indonesia than it did under Suharto, the authoritarian who used it as an instrument of power to keep a firm lid on Islamic activism. In that, the Australians would have been well advised to remove the offensive poster – rather than have an overzealous lieutenant turn it into a diplomatic incident.

John McBeth is the author of The Loner: President Yudhoyono’s Decade of Trial and Indecision