Having a separate chain of command for the Special Air Services Regiment operating in Afghanistan was in retrospect "possibly a mistake", a defence group admits.
There's allegations, raised in a confidential defence inquiry report obtained by Fairfax Media, that soldiers in the elite group may have committed war crimes in Afghanistan.
The inquiry was told of unsanctioned and illegal application of violence on operations and disregard for human life.
Australian Defence Association spokesman Neil James says for the first time at war, the SAS in Afghanistan did not fall under the command of the local Australian force commander.
"In retrospect, and in fact we've thought for a long time, that was possibly a mistake because you don't co-ordinate the operations well enough but also it doesn't allow a proper system, or as good a system, of accountability up the line," he told ABC radio.
He also pointed to problems with SAS soldiers to an extent being able to choose their own officers which produced "some interesting relationships".
The inquiry into allegations was commissioned by the then head of the SAS two years ago.
Another investigation by the Inspector-General of the Australian Defence Force will recommend how to deal with the claims.
Mr James predicted soul searching from the bottom to top when the findings are released, and the rolling of heads if failings are identified.
He also pointed to Canada's decision to disband its airborne regiment in 1995 over the conduct of soldiers on peacekeeping missions in Somalia and the hazing of young officers.
"I don't think anyone's suggesting the SAS Regiment be disbanded but obviously inquiries and ensuing action will have to be so far reaching we'll have to make sure that serious allegations like this ... never happen again," he said.