A former Garuda pilot at the helm of a plane that crashed in Indonesia, killing 21 people including five Australians, will "enthusiastically" fight criminal charges, his lawyer says.

Captain Marwoto Komar, 46, is expected to be formally charged on Thursday when his trial begins in Slemen District Court, in Yogyakarta in central Java.

He is expected to be charged with three alternative sets of offences over the 2007 Garuda crash at Yogyakarta Airport.

If convicted of the most serious charge - deliberately and unlawfully causing an accident or destroying a plane - he could face life in jail.

Komar's lawyer Mohammad Assegaf said it was the first time a pilot had been charged with a criminal offence over a plane crash.

"Marwoto is really eager to get confirmation of his status, to be cleared and confirmed," Assegaf said.

"He has been investigated and has to report (to authorities).

"This trial would answer these questions - he is really enthusiastic for the trial."

Assegaf said the move to prosecute Marwoto was "frightening" for many pilots.

"Why must an aeroplane accident be charged as a criminal act - this has only happened here, it has never happened before in any other country.

"Why not follow the marine way - in maritime (accidents) there is a marine court and the sanction it's only administrative.

"Why is it that there is no such court for pilots, and he has become a criminal?"

Five Australians - diplomat Liz O'Neill, AusAID official Allison Sudradjat, Australian Federal Police Officers Brice Steele and Mark Scott, and Australian Financial Review journalist Morgan Mellish - were killed in the March 7, 2007 crash.

They had been travelling to Yogyakarta for an official visit by the then foreign minister Alexander Downer.

Five judges will hear the case, which is expected to run for several months.

A final report by safety regulators said the pilot was so "fixated" with landing that he ignored 15 alarms and the pleas of his copilot warning that he was coming in too fast.

Marwoto's arrest in February shocked Indonesia's aviation community and sparked protests outside parliament demanding his release.