The elite troops, including the Special Air Service Regiment, served in the country alongside US-led forces between 2001-14.

A 2016 report by a consultant commissioned by the defence force and revealed by Fairfax Media on Friday made explosive allegations of "unsanctioned and illegal" violence by elite troops while on operations.

The report -- which also said there was a "perception of a complete lack of accountability at times" -- prompted a second and continuing probe into special forces actions in Afghanistan by the Inspector-General of the Australian Defence Force.

The third inquiry will see former Australian Security Intelligence Organisation chief David Irvine look into how further improvements could be made to the regiments since culture and governance reforms were implemented in 2015, the defence department said.

"The review will assist army leadership to determine the effectiveness of reform initiatives and identify whether additional improvements are required," a defence spokesman said in a statement.

Defence Force head Air Chief Marshal Mark Binskin said Friday of the probe by the Inspector-General that the "serious allegations... must be thoroughly examined independently from the chain of command".

"History has shown us that nations cannot become selective on what laws its military will or will not be held to account for," he said in a statement.

Some 300 Australian defence personnel remain in Afghanistan.