Military data has revealed more than a third of female recruits reported sexual misconduct while attending the Australian Defence Force Academy (ADFA) in Canberra.

According to a 2021 workplace survey, almost two-thirds of women at ADFA also reported being subjected to "any unacceptable behaviour", while a quarter of female recruits experienced bullying.

The research, first tabled in the Royal Commission into Defence and Veterans Suicide, showed almost 30 per cent of recruits who experienced unacceptable behaviour took no action, with many reporting it was "accepted around here".

Defence Chief General Angus Campbell has been challenged about the findings by Greens Senator David Shoebridge during a Senate estimates hearing in Canberra on Thursday.

"All of this is bad. All of this should be reduced as far as possible. All of this should be seeing the encouragement for individuals to be confident to make a complaint," General Campbell said.

The defence chief said he was also concerned that the military justice system was often letting off offenders convicted of indecent assaults with small fines and reductions in rank.

Senator Shoebridge told the committee recent data from the Judge Advocate General (JAG) revealed those cases "almost never ended in dismissal" and offenders' records were "wiped" when they entered civilian life.

General Campbell said he had been aware of the "defect" in the military justice system issue for "some time" and was concerned about it, but had not raised the issue with Defence Minister Richard Marles.

"No, I have not done anything because it is not within my purview to do anything … this is a matter for the Judge Advocate General," General Campbell said.

Asked whether women were being deterred from joining the military because of the ADF's workplace culture, General Campbell conceded it could be one factor.

"It may be a consideration by potential applicants and indeed families of those applicants, amongst a range of other considerations, some that might encourage and some that might discourage application to serve."

Further problems exposed with HMAS supply during estimates hearing

One of the Royal Australian Navy's newest warships could be out of service for another year as Defence works to repair a "complex defect" that has already hampered the vessel for more than a year.

In March last year, the ABC revealed that Spanish-built ship HMAS Supply had to be taken in for mechanical work that is being paid for under warranty by the Navantia company. 

Rear Admiral Steve Tiffen told the Senate estimates hearing that Navy had since discovered that another spare part needed to be ordered from Europe, which could take up to 40 weeks to arrive in Australia.

"It's called the intermediate shaft, somewhere between the gear box and the propeller shaft and that's a 15-metre-long, 19-tonne, half-a-metre-diameter shaft," the navy's head of maritime sustainment said.

Greens Senator David Shoebridge said: "The sort of thing you should get right the first time you pop it in a ship, isn't it?"

"Absolutely," Rear Admiral Tiffin replied.

Navy Chief Vice Admiral Mark Hammond told the committee estimates he wanted the $670 million ship, which first entered service in April 2021, back on operations as soon as possible.

"This is a complex defect. Navantia have written to the department accepting liability, it will be repaired under warranty."

"I do not want the committee to get the wrong idea, I am not satisfied with the availability of this ship," the navy chief added.