The Defence Force Chief (CDF) has clarified that a special forces soldier who allegedly threatened a female Australian spy with a handgun in Afghanistan is not facing further action over the incident.

The ABC revealed details of the incident in October after a report by the Inspector General of Intelligence and Security (IGIS) referred to a serious "incident overseas".

It was reported earlier today that Air Chief Marshall Mark Binskin told a Senate hearing the man had been charged.

But the Defence Chief later clarified the soldier had been charged in relation to separate allegations of misconduct.

"Nine ADF personnel have been charged under the Defence Force Discipline Act, including the defence member who was the subject of the original allegation," Air Chief Marshall Binskin said.

"Given that the matter is currently under consideration it is not appropriate for me to provide further details, but I just wanted to clarify that."

On the earlier allegation relating to a hand gun, the CDF said no further action could be taken based on the available information.

"However a further assessment will be undertaken if further information becomes available to that," he said.

Scant details of the incident emerged in October in the annual report of IGIS head Dr Vivienne Thom.

"While no physical injury resulted, the incident had the potential to cause serious injury," the report said.

The ABC confirmed the incident involved a trooper from Australia's elite Special Air Services regiment pulling a handgun on an ASIS agent.

Both the soldier and the agent had been drinking. Both were armed.

Another source confirmed the agent was a woman.

The trooper was part of a defence support team assigned to protect ASIS agents working in high-threat environments.