The man was arrested on Monday by Australian Federal Police after a years-long inquiry into alleged war crimes committed by Australian Defence Force personnel during the Afghanistan war.

Oliver Jordan Schulz, 41, was charged with one count of war crime murder in the Queanbeyan Local Court on Monday.

Schulz did not apply for bail and was remanded in custody.

Australian Federal Police said Schulz was alleged to have murdered an Afghan man while deployed in Afghanistan.

The charge carries a maximum penalty of life imprisonment.

Schulz is expected to face the Sydney Downing Centre Local Court on May 16.

The ex-SAS soldier was awarded the Commendation for Gallantry for his service in Afghanistan.

He had been working as a manager for the Royal Australian College of General Practitioners' (RACGP) Future Leaders program.

An RACGP spokesperson said it was "acting appropriately" following the news of the arrest of one of its employees for a "very serious crime".

"We are aware that one of our employees has been arrested in New South Wales and that this is of course a very serious matter," the spokesperson said.

"We were not aware this issue when he became an employee of the RACGP.

"As for his ongoing employment, we will manage that as an employment matter and address it directly with him."

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Monday's arrest marks the first in relation to the "credible" findings of war crimes as revealed in the 2020 Brereton report.

Justice Paul Brereton's four-year enquiry revealed credible evidence that 25 special forces personnel were involved in the unlawful killing of 39 individuals, mostly prisoners, farmers and civilians.

The Office of Special Investigations was established in late 2020 to begin its investigations into the alleged war crimes following the report's recommendations.

The office's director-general, Chris Moraitis, told senators in February his team was investigating "between 40 and 50" alleged offences and expected to hand Commonwealth prosecutors a brief by mid-2023.

"Investigations are under ongoing review and that number may increase if additional matters are raised, but over time I expect it will reduce overall as it becomes clear which allegations may be substantiated to the high threshold required for a criminal justice process," he said in an estimates hearing.

"As always, we are conscious of the potential impact on anyone affected by our investigations and my teams are unwavering in their commitment to ensuring allegations of war crimes within our remit are subject to fair, thorough and impartial investigation without unnecessary delay.

"War crimes investigations are inherently complex, but I remain optimistic a first full brief of evidence will be ready for the Commonwealth Director of Prosecutions to consider in the months ahead."