An Australian soldier suspected of overdosing on drugs in Afghanistan has been flown back to Australia for further medical treatment.

The soldier was being treated in a US medical centre in Germany after he was found unconscious in his room in Tarin Kowt late last month.

The Defence Department says the soldier's health has improved but he remains in a serious condition.

Defence says the soldier is being supported by his family, who have asked for privacy.

It also plans to hold an inquiry into the circumstances of his ill health.

The soldier, known as Private D, was described by Air Chief Marshal Angus Houston as a courageous and "very professional" soldier whose actions had once saved the live of a mate.

Private D joined the ADF in 2004, has served in East Timor and was on his third deployment to Afghanistan.

A Chief of Defence Force commission of inquiry into the incident, to be headed by a civilian, is soon to be established.

The inquiry, on Defence Minister John Faulkner's instructions, will also examine how soldiers may be obtaining illegal drugs, deficiencies in the current drug testing program and whether mental health services available to soldiers in theatre need to be improved.

An Australian Defence Force Investigative Service (ADFIS) investigation is also underway.

And the acting Commander of Australian Forces in the Middle East, Commodore Roger Boyce, will also investigate circumstances surrounding a function the sub-unit was at the evening before at which they were given permission to drink alcohol.

Air Chief Marshal Houston said he had never held concerns about the use of narcotics by soldiers on operations until now, but there had been "targeted" testing in relation to other substances such as steroids.

There are around 1,500 Australian soldiers serving in Afghanistan.