The Defence Force says the conduct of one soldier fell below its standards while on patrol in Afghanistan in 2004.
The military is responding to allegations made in the Stuff documentary The Valley, which was broadcast in 2017.
It accused SAS forces of committing offences - including aggressive interaction with villagers, mistreating dead bodies, damaging property, as well as unreasonably detaining and mistreating civilians.
A review by Defence Legal Services has cleared the military of some of those claims.
However, on the allegation of civilian mistreatment, the review found the conduct of one unnamed soldier fell below military standards.
The Defence Force said the allegation did not reach a threshold to proceed with a criminal prosecution.
It said on Monday, the chief of defence Kevin Short ordered a review of military training, as well as developing a specific policy related to civilian causalities.
Air Marshal Short said the allegation of civilian mistreatment came to light during the military's investigation after the documentary aired.
He said the male soldier was accused of pulling the clothes off a male civilian when soldiers were detaining and questioning locals.
"They needed to restrain those individuals to ask questions about what had occured the night before.
"The clothes that were being worn by the male (civilian) fell off basically... there were a number of people who tried to flee - or resisted - and so they were restrained by putting plastic cuffs on," he said.
The unclothed civilian was not injured, he said.
The Military Police investigated and recommended to the soldier's commanding officer that charges be laid.
Air Marshal Short said the problem was there was only one witness statement and more than a decade had passed.
A couple of reviews were conducted by the commanding officer, however, there had been no criminal prosecution.
"There was no applicable charge which would likely lead to a conviction."
However, he said administrative action was taken and a note was put on the soldier's personal file last year.
He said the soldier has since left the military.