"No, I can tell you with confidence, he hasn't had anything to do with the Taliban," he said.
"When I heard about this incident, I was stunned.
"I would like to express my condolences to the families of those Australians who have been killed."
Afghan National Army member Darwish Khan shot ten Australians as well as a number of Afghans, reportedly opening fire with a machine gun.
His father also told the ABC's Sally Sara that his son was only recently married.
Hundreds of Afghan soldiers were stripped of their weapons and confined to their barracks after Khan killed Corporal Ashley Birt, 22, Lance Corporal Luke Gavin, 27, and Captain Bryce Duffy, 26.
The Afghan National Army soldier gunned down the Australians as they were on morning parade in Kandahar province.
A corporal, captain and lance corporal were killed, making it the single most deadly attack on Australian forces of the entire Afghanistan campaign.