Indonesia's President Joko Widodo reproached his military chief in a meeting last week amid concerns the commander was "out of control" after he unilaterally suspended defence co-operation with Australia, two sources briefed on the meeting say.
Widodo's intervention highlights alarm about General Gatot Nurmantyo, who promotes the notion that Indonesia is besieged by "proxy wars", in which foreign states seek to undermine the nation by manipulating non-state actors.
Analysts and some of Widodo's aides are also concerned that Nurmantyo is laying the groundwork for an expansion of the military's role in civilian affairs in the world's third-largest democracy and may have political ambitions himself.
Widodo, the first president from outside the military and political establishment, needed to move quickly to demonstrate his authority as the country's commander-in-chief, one senior government official said.
"With Gatot, the feeling is like he's a little out of control," he said.
Nurmantyo declared a rupture in military ties after an Indonesian officer found "offensive" teaching material while on a language training course in Australia late last year.
The material suggested that Indonesia's Papua province should be independent and mocked the nation's state ideology, Pancasila, according to Nurmantyo.
One of the officials told Reuters Widodo and others in the government were caught off guard when local media reported Nurmantyo's announcement of the suspension in military ties with Australia.
While the general was not formally reprimanded, the official said, Widodo served him a warning during a meeting at a presidential palace in Bogor, outside Jakarta.
The meeting was confirmed by another senior government aide, who also spoke on condition of anonymity.
Nurmantyo declined requests to be interviewed and a military spokesman declined to comment on the meeting.
The senior government official said: "We suspect that Gatot is exploiting this incident for his own political agenda, his own political ambition."
"He has been making many public appearances and speeches lately," he said.
"Frankly, we think many of them about proxy wars and the threat to Indonesia are absolutely ridiculous."
In one speech, Nurmantyo predicted that a food shortage in China could trigger a flood of boat-borne refugees.
He told listeners he would slaughter 10 cows and dump them into the sea to attract sharks that would devour the Chinese.
One of the officials who disclosed Widodo's meeting with Nurmantyo said the military chief's job was safe, downplaying speculation that the general would be relieved of his duties.
"For now, we are confident that he will not betray the president or the civilian government," he said.
The ABC reported last week that Nurmantyo told an audience in Indonesia recently he believed the Australian military was attempting to recruit Indonesian soldiers sent to the country for training.
Australian Defence Minister Marise Payne rejected the allegation.
Australia's defence co-operation with Indonesia spans some of the most controversial issues in domestic and international politics today, including the fight against terrorism, refugee and asylum seeker movements, the South China Sea and cyber security challenges.
Indonesia's move to suspend all military co-operation with Australia is the latest in a series of disputes between the two neighbours and risks the careful progress talked up by the Turnbull government and President Joko Widodo's administration.
What is included in Australia's formal co-operation agreements with Indonesia?
The most recent 2+2 Dialogue with both countries' foreign and defence ministers in October 2016 highlighted a "comprehensive strategic partnership with the objective of ensuring economic development, prosperity, peace and security in the region."
As part of recent agreements, Australia has reiterated support for Indonesia's territorial integrity and sovereignty and agreed to work with Jakarta on maritime security, intelligence, humanitarian assistance and disaster relief as well as capability development and procurement.
Indonesia has welcomed Australia's recent white paper on the development of northern Australia and agreed to increased defence industry and military modernisation co-operation to promote peace, stability and security in the Indo-Pacific region.
The two countries complete regular military training together, with joint exercises and exchanges. They co-operate directly on controversial anti-people smuggling operations and on anti-radialisation efforts such as trying to stop foreign fighters joining overseas conflicts, including with Islamist groups in the Middle East.
The first joint training exercise on Australian soil since 1995 took place in Darwin last year. It was considered a landmark event in the repair of the relationship since the East Timor crisis.
The two countries have acknowledged a common threat from terrorism and established links between law enforcement and national security agencies, immigration and customs bodies and cyber security experts.
In October Defence Force Chief Air Chief Marshal Mark Binskin hosted Indonesian National Armed Forces Commander, General Gatot Nurmantyo, in Canberra, as part of efforts to promote "mutual trust and cooperation".
On Thursday, Defence Minister Marise Payne said only some aspects of co-operation had been put on ice and negotiations about Indonesia's involvement in a multilateral military exercise planned for next month were ongoing.
Jakarta: Indonesia's foreign ministry says President Joko Widodo hopes to visit Australia in the first three months of this year in an indication the furore over offensive material at an Australian army base has not damaged the wider bilateral relationship.
"We are still trying to find a date suitable for both leaders … there is a strong commitment from both sides to meet in the first quarter of this year," Foreign Ministry spokesman Arrmanatha Nasir told Fairfax Media.
President Jokowi, as he is popularly known, postponed his state visit to Australia last year after a rally in November calling for Jakarta's Christian governor to be jailed for alleged blasphemy ended in violence.
Prime Minister Malcolm Turnbull said Australia would always warmly welcome a visit. "President Widodo has indicated his desire to visit and officials are actively working to find mutually convenient dates to reschedule the visit postponed in late 2016," he said.
The Australian Defence Department has also confirmed that Exercise Cassowary, an annual training exercise involving Indonesian and Australian naval patrols, would proceed as planned.
"The Royal Australian Navy has a series of bilateral exercises and activities with Indonesia in the coming months," a spokesman said.
"There have been no recent changes to scheduled exercises or planned activities."
Meanwhile, Foreign Minister Julie Bishop has stressed the Australian government takes seriously its obligations regarding the safety and security of foreign diplomats and diplomatic premises after a trespasser waved a West Papuan separatist flag on the roof of the Indonesian consulate-general in Melbourne on Friday.
The incident, which The Jakarta Post described as a "fresh snag" in Indonesia and Australia relations, occurred just days after Indonesia's military chief revealed suggestions that West Papua should have independence was among curriculum he described as "too painful to explain" that was being taught at a Perth army base.
The offensive material caused a suspension in defence ties between the two countries, although chief security minister Wiranto clarified late on Thursday that this only related to a language training program and military cooperation had not been completely severed.
Foreign Minister Retno Marsudi said the break-in at the Indonesian Consulate General building on Friday was a "criminal act that is completely intolerable".
She said in a statement she had communicated with Ms Bishop on Saturday to ensure the Australian government would conduct an investigation and legal process against the perpetrator of the crime.
"The 1961 Vienna convention … states that "the receiving state is under a special duty to take all appropriate steps to protect the premises of the mission against any intrusion or damage and to prevent any disturbance of the peace of the mission or impairment of its dignity."
Flying the separatist West Papuan "Morning Star" flag is banned in Indonesia, which is sensitive about the pro-independence movement and allegations of human rights violations in the restive province.
Mr Nasir told Fairfax Media the main concern was that the trespass was able to occur in a known diplomatic area, with the offender clambering over a wall from a neighbouring private property.
"If they are doing this within the context of the law it's fine, but the concern here is they are breaking the law and the security of the consular mission," he said.
He pointed out the trespasser was Caucasian and not related to Indonesia.
Mr Nasir said Ms Bishop had given a strong commitment that Australia would act urgently to apprehend the trespasser.
An Australian Federal Police spokesman said investigations remain ongoing. It is understood charges are yet to be laid.
Bob Lowry, the author of The Armed Forces of Indonesia, said there was still a lingering suspicion that Australia would change its mind and support an independent West Papua after its intervention in East Timor.
"Despite the Lombok treaty, a lot of people are very concerned about that," he said.
"They don't want a situation to open up in which large scale movements in support of that aspiration (independence) develop in places like Indonesia and Australia."