Any further political rise of the head of Indonesia's armed forces, General Gatot Nurmantyo, could be a threat to Australia's vital military relationship with Indonesia, Australian Strategic Policy Institute head Peter Jennings said, adding he thought it was 'alarming' that the General appeared to be questioning the ties.
After General Gatot announced on Wednesday all military co-operation between the two countries was affected, Indonesia softened its stance on Thursday night when a senior minister said the ban only applied to the special forces classes which sparked the diplomatic row.
Australian National University Indonesian Politics Associate Professor Greg Fealy said this would have come straight from Indonesia's President Joko "Jokowi" Widodo and constituted "a complete back down".
Jokowi is just being a bit delicate about it but the intent of what he did was unmistakeable. He said that yes Indonesians must not be insulted by other countries, but nonetheless he instructed his coordinating minister to go and make a very clear cut public statement that the disruption was just restricted to language training. We saw the president put back in his place the head of the armed forces," he said.
Mr Jennings, a former Deputy Secretary in Defence, said while the current spat is unlikely to have a major long term impact on relations, it was alarming that they looked so fragile and General Gatot appeared to question the worth of the ties.
"It has always, certainly in the last 10 years, it has been the defence relationship that has been the stable element of bilateral relationship even when there has been problems at the political level.
"So what's been alarming about this incident is what used to be considered to the the sort of pillar of stability in relations which was the mil to mil contact seems to be now questioned by this individual," he said.
Mr Jennings said it would be damaging if General Gatot succeeded in any political ambitions he might have.
"If that is where he's heading then maybe that is going to complicate the defence relationship but it sounds to me like it would also complicate their relationship with the US and China," he said.
General Gatot said on Thursday that the reason he made the decision to suspend military co-operation was there were "hurtful" teaching materials saying that West Papua, which Australia recognises as part of Indonesia, should be independent and other materials mocking Indonesia's founding principles, the Pancasila.
While Defence Minister Marise Payne refused to confirm what the materials contained, she said they were removed and suggested they were not "culturally appropriate.
Now, Greens leader Richard Di Natale slammed Senator Payne over the decision, saying if they were about West Papua then Australia had "betrayed" residents of the region which Australia officially recognises as part of Indonesia under the Lombok treaty.
"The government had the opportunity to show some integrity and stand up for the human rights of the West Papuan people but instead they betrayed them. Rather than rewriting our military training manuals we should be rewriting our policy to help end one of the longest-standing human rights crises in our region," Mr Di Natale said.
Indonesian media has reported that Defence Minister Ryamizard Ryacudu said the headmaster of the language school at the SAS base at Campbell Barracks has been suspended.
But the Defence department said this was not so. "No, the principal has not been stood down. As Minister Payne has noted, the Army inquiry into the matter is not yet finalised," a spokesman for Defence said.
Indonesia's special forces had been participating in language courses at the Australian special forces base at Campbell barracks in Perth.