A senior Afghan commander made allegations last weekend about the treatment of four suspected members of the Taliban who were captured after Australian soldier Jason Marks was killed during an attack in Oruzgan Province.
The Australian commander for the Middle East, Major General Michael Hindmarsh, says the defence force takes its legal obligations on the safe and humane treatment of detainees very seriously.
He says information about the alleged incident is still being gathered.
The foreign minister, Stephen Smith, earlier told Australia Network that the outcome of the investigation will be reported directly to him, and has promised full transparency on the alleged incident.
"Australia takes very, very seriously any suggestions of misconduct by its combat forces in the field," he said.
"I have asked to be kept informed of the outcome of those investigations, and our army personnel, the chief of our defence forces, has made it absolutely crystal clear that we do not countenance in any way, inappropriate conduct by our forces in the field".
The head of Australia's military, Air Chief Marshal Angus Houston, says he became aware of the allegations last weekend.
He says he immediately organised the establishment of two inquiry teams.
"One was a police team, an ADF investigation team, and a second team which was an administrative team that would do an inquiry under the defence instructions that relate to inquiries," he said.