A service was held in Sydney today to commemorate 50 years since Australian troops departed for the Indonesia Confrontation in Malaya.

Between 1962 and 1966, Indonesia fought a small, undeclared war with Malaysia in an effort to destabilise the new federation.

The conflict resulted from a belief by Indonesia's then-president Sukarno that the Malaysian federation was an attempt by the British to maintain rule while appearing to be granting independence to the former colony.

The term Konfrontasi – meaning confrontation – was coined in 1963 by Indonesia's foreign minister at the time, Subandrio, and came to refer to Indonesia's attempt to destabilise and break up the new federation.

The war, which began when Indonesia launched a series of cross-border raids into Malaysian territory in early 1963, came to involve Australian troops under British command.

At the time, cross-border operations were top secret, and the conflict received very little coverage in the Australian press.

About 300 Malaya and Borneo veterans today commemorated 50 years since HMAS Sydney left Garden Island bound for the conflict.

Veteran Adam Henderson said their service had largely been overlooked.

"There were certain things that were done there that, for diplomatic reasons – that's what was explained to us – would embarrass the Australian government," he said.

"A lot of the actions or incidents that occurred were handed back to the credit of the local Malay constabulary or the military."

Another veteran, Norman Park, said the secret nature of the operation left Australian troops feeling "shut out".

"As far as I'm concerned, it was much like the Korean war," he said.

"We couldn't say much about it. We were tied."