The strategy, launched by Employment Minister Michaelia Cash on Thursday, called for an "honest stocktake" of failures to ensure staff are granted equal opportunities and merit is appropriately rewarded.

It comes a week after Prime Minister Malcolm Turnbull warned bureaucrats he expected more leadership to be shown on gender equality, deeming it a critical task in coming years.

The strategy called for departments to strive for a 50-50 gender balance across the workforce with senior staff tasked with supervising and reporting on progress.

Management have been told to promote flexible work arrangements more common in the private sector to ensure senior staff can manage work and family responsibilities.

Senior leaders will be trained and tasked with removing unconscious gender balance with some to be seconded to areas of the workforce with high inequality.

Management have also been told to prioritise the recruitment of women in areas such as science, IT and finance which have historically had few women.

But the task of reform is far from easy. Women account for 58.7 per cent of the federal bureaucracy but represent just 41.8 per cent of the senior executive service.

Implicit bias also remains a barrier for women being recruited to senior roles.

At the Department of Foreign Affairs and Trade, 57 per cent of the workforces are women but they only account for 27 per cent of heads of mission.

DFAT secretary Peter Varghese said embracing reform would ensure staff could reach their potential and the department could improve productivity.

"Unequal representation of women at our senior levels suggested that despite equal recruitment since the mid-1980s, there were factors inhibiting many of our female colleagues achieving senior roles," he said.

The report found women were less likely to have informal networking opportunities than men, often forcing them to" miss out on the connections and confidence these offer".

While flexible work arrangements are available at most agencies, the report found they were almost entirely accessed by women and by few senior leaders.

"Flexible work is seen largely as an accommodation for women and as incompatible with working in a leadership role," the report said.

Men are twice as likely to be denied flexible working arrangements and account for 18 per cent or all part time staff across the public service

When Mr Turnbull spoke to 800 mostly senior public servants at Parliament House last week, he described workplace flexibility as "absolutely critical".

"As a leader, as a manager, of a business, a department, a unit or a section, part of your job is, as far as you can, to make sure that the people you are responsible for are able to get the right balance between home and work," he said.

In the report, Department of Employment secretary Renee Leon described flexible work conditions as an important step to ensuring women could rise up the ranks.

"For too long the norm has been one that assumes our staff don't have family responsibilities," she told the report.

Department of Defence secretary Dennis Richardson acknowledged his workforce ranked poorly for gender equality when compared to others.

"Increased female participation in the Defence APS workforce, and in senior leadership roles, must be a focus if we are to broaden our access to the considerable skills and capabilities within the Australian community," he said.

According to the latest APS State of the Service report, the number of women employed at an SES 3 rank has increased five-fold since 1995. Back then, women represented just 19 per cent of the SES ranks.

Three years ago, women accounted for 39.5 per cent of SES positions across the workforce. This was significantly higher than the 16.4 per cent of women serving on the boards of ASX 200 companies.