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.

Happier times: General Gatot Nurmantyo and Australian Defence chief Air Marshal Mark Binskin after signing a statement on defence co-operation in October. Defence Department

"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.