An Australian Special Forces soldier has died in a non-combat-related incident in Afghanistan, Defence Force Chief Mark Binskin has announced.

Air Chief Marshal Binskin said the soldier's colleagues found him in an administration building with a gunshot wound.

The soldier was evacuated to a medical facility in Kabul, where he underwent medical treatment, but died of his injuries.

"Sadly, the soldier's injuries were too severe and he later died surrounded by his mates," Air Chief Marshal Binskin said.

"On behalf of the Australian Defence Force, I offer my condolences to the family, the friends and the colleagues of this brave soldier.

"He was a highly qualified, experienced and well-respected Special Forces soldier. His death will impact the nation and we will do all we can to support his family."

The facility was locked down overnight so coalition military police could collect evidence and the Australian Defence Force investigative service has also begun its inquiry.

Air Chief Marshal Binskin stressed that the facts surrounding the soldier's death remain unclear.

The soldier's family has requested privacy and that his name not be released.

"We are deploying a psychological support team to Kabul to provide additional support," Air Chief Marshal Binskin said.

Asked whether he was confident Defence is doing enough to treat post traumatic stress disorder, Air Chief Marshal Binskin said he was "confident" in Defence's general management of mental health issues.

"But in this particular case I won't speculate," he said.

"I need to let ADFIS [Australian Defence Force Investigative Service] determine the facts in the investigation and then can make some decisions."

Deputy Prime Minister Warren Truss says 400 Australians remain on duty in Afghanistan.

"We don't know a great deal about the details as yet. I certainly extend sympathy to the family and friends of the soldier we have lost," he said.

"It is a tragedy after Australia's official engagement has been wound down that we should lose another Australian in Afghanistan."

The Sydney-based 2nd Commando Regiment soldier is the 42nd Australian to have died during the Afghanistan conflict and the 41st from the Australian Defence Force.

The 2nd Commando was the same regiment of Victoria Cross recipient Corporal Cameron Stewart Baird MG.