Australia's special forces will have a new strengthened command structure to prepare for a "challenging decade ahead".
The leadership of the Special Air Service will be elevated to colonel to provide the Perth-based regiment with additional experience.
It has previously been led by a lieutenant colonel.
Defence Minister Peter Dutton says the change will increase the qualifications and experience of those overseeing sensitive operations.
"This is a critical reform to prepare the SASR for future conflict, getting them back to basics and focused on the challenges ahead," he said on Wednesday.
"We have seen the skill and acts of bravery of the SAS in just the last week from the work that they have done (assisting with evacuations) in Afghanistan. Those men and women who serve in the SAS are an incredible asset to our country."
The move comes after the Brereton inquiry last year found credible evidence Australian troops murdered 39 people in Afghanistan and uncovered allegations of torture and other war crimes.
Chief of Defence Angus Campbell considered disbanding the entire SAS regiment after receiving the exhaustive report, ultimately opting to disband just one of the squadrons embroiled in the allegations.
A group of 13 soldiers has since been told there is insufficient evidence for their cases to be referred to investigators after being told to prove why they shouldn't be sacked.
An investigation by the Office of the Special Investigator remains active.
Former SAS captain and assistance defence minister Andrew Hastie said the leadership change reflected a "new era" for the regiment, which marks its 75th anniversary this weekend.
He said the environment the SAS operated in was growing in complexity, with Australia likely to face more "grey zone" missions in the future.
"This is a vote of confidence," he told 2GB radio.
"Today is a day where we're celebrating a sort of new dawn for the SAS. The ladies and gentlemen of the SAS are very focused on their task and I can sense a rise in morale."