Results from the Australian Defence Force's 2023 Workplace Behaviours Survey were only publicly released because of an order from the Senate.
"Between 2019 to 2023, a larger proportion of women than men experienced unacceptable behaviour," the report reads.
"This difference is statistically significant in each year.
"Women are significantly more likely than men to make a complaint about behaviour that they experienced."
The survey found one in five women in Defence made a complaint about unacceptable behaviour.
It also found Navy results tended to be negative for a range of areas including work-life balance and morale.
"Intention to leave shows a consistent pattern of increase over the past four years, with the highest intention to leave across all groups and services," it found.
The Royal Commission into Defence and Veteran Suicide, which handed down its final report earlier in September, recommended an independent inquiry into sexual violence.
The inquiry found troops convicted of sexual crimes under the military justice system remained in service, with the ADF not knowing how many of its members had been convicted in civilian courts - even when the offending was against another defence force member.
Veteran's Affairs Matt Keogh says there is no level of acceptable misconduct in the military. (Mick Tsikas/AAP PHOTOS)
Defence Personnel Minister Matt Keogh said sexual misconduct, harassment, bullying was unacceptable.
"We're not happy to see any of those statistics at all," he told reporters.
"There is no level of acceptable misconduct. We want to see that stamped out."
Greens defence spokesman David Shoebridge said the data showed senior leaders had failed to deal with misconduct.
"My office keeps hearing from veterans and families of veterans about the toxic culture in Defence and the need for immediate change,'' he said.
"Veterans give years of their lives to the ADF only to feel abandoned both during service and after.
"This data should be used to remove senior staff who have failed to provide safe and inclusive workplaces, but instead of this Defence tried to bury it and hide the truth from parliament and the public."
Mr Keogh met state and territory leaders responsible for veterans' issues in Canberra on Friday, where they agreed to strengthen cooperation following the royal commission's final report.
They will work together to improve services and supports for the veteran community and said a timely response was needed to the inquiry's recommendations.
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