Defence Minister Richard Marles said the decision -- related to specific unit commanders who were in charge between 2005 and 2016 -- was needed to "address the wrongs of the past".
Fewer than ten commanders will be stripped of their awards, but their names will not be released for privacy reasons.
An official inquiry into the 11-year period examined the alleged unlawful killing of 39 civilians and prisoners in Afghanistan by Australia's elite special forces.
Its findings in 2020 revealed a "sub-culture of elitism and deviation from acceptable standards", Marles said, which "warranted the most serious, considered and thorough response".
Almost all the report's 143 recommendations have been adopted -- including a medal review, a compensation scheme and culture reform.
The inquiry also suggested 19 individuals be referred to Australian Federal Police, but this process has been slow.
Police have so far only pressed charges against a former SAS soldier -- whose case remains before the courts.
Ex-SAS corporal Victoria Cross recipient Ben Roberts-Smith notably lost a defamation case last year over allegations he had murdered four Afghan prisoners.
But he has not faced criminal charges and is not identified in the government's report over any wrongdoing.
Despite being decorated for his service in Afghanistan, Roberts-Smith is not understood to be affected by the latest decision to strip unit commanders of their honours.
- 'Accountable' -
Marles said the commanders involved in Thursday's decision may not have been aware of the war crimes their units allegedly carried out, but there was an expectation for them to know what was happening.
He vowed to continue reforming the defence force culture and police have not pressed charges.
"Australia is a country which holds itself accountable," Marles said.
The governor-general of Australia -- the king's representative in the Commonwealth -- will determine how and when the medals are handed back.
Greg Melick, president of the Returned and Services League of Australia veteran support group, said no medals should be taken away from recipients until all investigations and potential trials have been completed.
Melick said the incident had caused "significant strain" to veterans' mental health -- even those not involved in alleged incidents.
After the September 11, 2001 attacks, more than 26,000 Australian uniformed personnel were sent to Afghanistan to fight alongside US and allied forces against the Taliban, Al-Qaeda and other Islamist groups.
Australian combat troops officially left the country in late 2013, but since then a series of often-brutal accounts have emerged about the conduct of elite special forces units.
lec/djw/mca
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