Indonesia stopped sending its best soldiers for training in Australia because of fears they would be "recruited" by the Australian military.
Indonesia's military chief General Gatot Nurmantyo said he stopped the training program before suspending all military relations between the two nations.
In a speech from late November uncovered by the ABC, he made his feelings clear:
"Every time there is a training programme — like recently — the best five or 10 students would be sent to Australia. That happened before I was chief so I let that happen," he said.
"Once I became chief commander of the national forces, it did not happen again. They will certainly be recruited. They will certainly be recruited."
The general used the language of the Cold War, talking about the soldiers being cultivated as sources or agents of influence.
It was revealed yesterday that Indonesia suspended all military cooperation between the two nations after an instructor with the Indonesian Special Forces [Kopassus] was offended by material that was part of a training course in Perth.
The material related to perhaps Indonesia's most sensitive topic — independence for West Papua.
"My officers were told to be assigned over there, to teach Indonesian," General Nurmantyo protested.
"It was taught there that Papua is a nation that is going to get their independence because they're not Indonesia. Like that. So clearly they will recruit them."
'A deeply offensive phrase'
Iwan Ong Santoso, an Indonesian author and journalist with Kompas newspaper, broke the story about Indonesia suspending its military relations with Australia.
He said the West Papua element was only part of the reason for the breakdown.
Mr Santoso said that when the Kopassus officer went to complain about the West Papua commentary, he discovered a document mocking Indonesia's key principle of Pancasila.
"We believe that our basic philosophy to build our nation is Pancasila, the five principles, and there was this writing of 'Pancagila'," Mr Santoso said.
"Pancagila is very insulting words of 'madness, insanity', saying like our nation has five kinds of insanity."
Pancasila is a statement of Indonesian unity, while a broad translation of Pancagila would be "crazy Indonesians".
It is a deeply extremely offensive phrase to an Indonesian.
Indonesia's Defence Minister Ryamizard Ryacudu said Australia had punished the person responsible.
"He's only a lieutenant," said Mr Ryacudu.
He said the Australian military and Government did not have the intention to insult or humiliate Indonesia.
He described those responsible as "curut" — which translates as mice. In other words, they are insignificant.
Mr Ryacudu said he would discuss the incident when he met with Australia's Defence Minister Marise Payne.