AFP Commissioner Andrew Colvin concedes the organisation has not done enough to promote women through the ranks and into high profile roles like that of ACT chief police officer.
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On Monday, the AFP released a report into its diversity, authored by former sex discrimination commissioner Elizabeth Broderick .
The report found "pervasive" sexual harassment and bullying in the organisation, in a finding that echoed revelations in the Australian Defence Force in recent years.
It found 46 per cent of women and 20 per cent of men reported being sexually harassed or abused in some way in the workplace, almost double the national average. Sixty-six per cent of women and 62 per cent of men said they had been bullied.
The study included the AFP's community policing arm ACT Policing.
It showed women are still vastly under represented, with sworn and unsworn members making up about 35 per cent of ACT Police.
And police women remain disproportionately represented in work areas that are predominantly support roles, the report says.
A common complaint was how difficult it was to work flexibly in operational response areas. One woman said if she had known about the shift work at ACT Police, she would not have joined because she wanted to start a family.
"There is pretty much no lee-way to change the arrangements here."
A male participant in the study said: "[In ACT Police] the rostering makes it hard for women with kids who don't work full-time. Because of the shift work, we can't easily grant flexible work, so it's easier for them to go to national."
Speaking to Fairfax Media, Commissioner Colvin said he could not single out ACT Policing from the other branches of the AFP.
"We're not saying there's a worse or a better cultural or behavioural problem with ACT Policing ... it's clear this report is saying we have issues across the breadth of the organisation.
"We are a male dominated force and unfortunately it's a male dominated industry. ACT Policing is also male dominated."
The ACT's top cop Rudi Lammers retires in December, and Commissioner Colvin said high-profile roles such as that were "ideal opportunities" to show the community the value of women in policing.
But a "pipeline issue" meant organisation had not done enough in promoting women to become candidates for those high-profile roles.
"I can't wave a magic wand and change our performance on diversity targets overnight," Commissioner Colvin said.
"Women live a very different experience in the AFP than men, and I need to level that playing field," he said. "It'll take time and it'll take time and lot of leadership and commitment.
"And that's why I've made this so public."
Mr Colvin said he would implement all 24 recommendations in the report, most urgently an independent office to investigate complaints and help victims, which he described as "a safe place".
