Among those charged is the trooper who drew the weapon on the female ASIS agent last December
The Chief of the Defence Force, Air Chief Marshal Mark Binskin, says he regards the case as a serious matter and the nine have been charged under the Defence Force Discipline act.
"I was very concerned about it.. as was the Chief involved, "Air Chief Marshal Binskin told a senate estimates hearing in Canberra.
"It was a very serious matter and we took it very, very seriously."
Not all of the nine ADF members were present during the incident which allegedly took place during a drinking session.
"As part of the investigation as we worked through this, there were allegations that came up," he said.
"Not directly with that, but other lower levels areas that we were concerned with as well. So we did not just look at one particular thing, we looked at the whole context of it."
The weapons incident emerged in the annual report of the Inspector-General of Intelligence and Security (IGIS), Dr Vivienne Thom.
The report revealed no-one was injured, but "the incident had the potential to cause serious injury."
Air Chief Marshal Binskin says administrative action against the nine ADF members is due to take place after the disciplinary action has been completed.
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