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Australian Prime Minister Malcolm Turnbull has condemned a photo showing an Australian army vehicle flying a swastika flag in Afghanistan.

The "completely and utterly unacceptable" incident took place during a mission in 2007, he said.

Military officials said the symbol of Nazism was up "briefly" before commanding officers intervened, adding that those involved had been cautioned.

It follows intense recent scrutiny of Australia's conduct in Afghanistan.

The photo of the 2007 incident caused anger after on Thursday.

"It was wrong - absolutely wrong - and the commanders took action at the time," Mr Turnbull told reporters.

In a statement, the ADF said it rejected "as abhorrent everything this flag represents".

The image shows soldiers sitting on the vehicle with the flag hoisted up at the front.

The ABC quoted an anonymous defence source who said the incident had been meant as a "twisted joke", rather than a sign of support for neo-Nazism.

Australia's conduct in the US-led coalition in Afghanistan has been scrutinised following media reports last week that elite soldiers may have been involved in the killing of unarmed Afghans.

The head of the ADF, Air Chief Marshal Mark Binskin, said the "serious allegations" would be investigated.

Australia's operations in Afghanistan are already the subject of a closed-door inquiry, which began in 2016.

Australia has about 300 troops currently in Afghanistan.