Retired general Angus Campbell was in charge of Australia's operations in Afghanistan during the time credible evidence was later uncovered about troops committing war crimes against 39 civilians.
Defence Minister Richard Marles revoked the medals and citations of up to nine soldiers in the chain of command who were not implicated in the alleged crimes but were part of command accountability as they oversaw the units.
Opposition Leader Peter Dutton is the latest to question why the general who went on to become the chief of the Australian Defence Force had kept his honours while lower-level officers lost theirs.
When in government as defence minister, Mr Dutton overturned a decision to strip an entire Special Air Service forces contingent of their meritorious unit citation after arguing the whole shouldn't be punished for the sins of a few.
On Friday, Mr Dutton asked why the retired general, who holds a Distinguished Service Cross, wasn't included in the chain command accountability affected by Mr Marles' decision.
"Why is it OK to throw, sort of, lower ranked diggers under the bus, but those who are higher up the chain avoid any scrutiny?" he told Nine's Today Show.
Questions have been asked why retired general Angus Campbell didn't also lose his honours. (Lukas Coch/AAP PHOTOS)
Mr Marles defended his decision to revoke the medals and citations, saying he followed "to the letter" the recommendations of the landmark report that uncovered the full breadth of war crime allegations.
"That simply is because it was Major General Brereton and his team which undertook the hundreds of interviews, which received the thousands of pages of testimony," he said.
The report alleged 25 Australian SAS troops were embroiled in potential war crimes and recommended those in the chain of command, despite not being criminally liable, lose their honours.
Investigator Paul Brereton put forward three levels but then-general Campbell's rank wasn't covered.
Veterans groups have come out against the revocations, with Martin Hamilton-Smith from the Australian SAS Association calling it "disgraceful".
It was a betrayal of the courage and sacrifice of Australian soldiers sent to fight and die in Afghanistan, he told AAP.
The Brereton report was being treated as a finding of guilt, despite the absence of a proper legal process, he said, and called for the final decision to sit with the governor-general.
He described the approach as "outrageous and unjust", saying accused soldiers had a right to their day in court.
But Australia Defence Association executive director Neil James thinks the anger is overblown, saying the process was no different from that for other awards.
"This is just part of the whole process that is going on - it shouldn't be a shock to anyone but it's being painted as somehow being unfair," he told AAP.
"The Brereton report itself stated while none of the commanders were legally responsible, they were morally responsible, so in all good conscience the medals can't be retained," he said.
Soldiers had a chance to state their case when told their accolades were under threat and some voluntarily handed theirs back.
"I can't understand the emotiveness some people are putting into this," he said.
Martin Hamilton-Smith has described the loss of citations and medals as "outrageous and unjust". (David Mariuz/AAP PHOTOS)
Command accountability was crucial to restoring Australia's international reputation, he said.
Independent Senator Jacqui Lambie, a former soldier, wants people higher in the chain of command held to account.
If commanders were not aware of the alleged crimes they should have been, she said.
The timing of the announcement was also widely criticised by veteran groups and politicians for coming just days after the release of a damning royal commission report into suicides among veterans and a broken defence support system.
Mr Marles said it was important to close the government's response to a dark chapter in Australia's military history in a timely manner after he made the decision.
"Whenever we were doing it was going to be a difficult moment but it was important that we do this," he said.
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