The warning comes after Employment Minister Michaelia Cash launched a four-year strategy to overhaul a culture of gender bias and inequality and start an "honest stocktake" of policies.

Deborah May, who has been helping agencies including Treasury and the Department of Defence improve gender equality for decades, believes leadership and accountability will dictate the success of the strategy.

"There has to be leadership around this," she said. "It has be driven from the top and when there isn't consistent leadership there is often cynicism and scepticism.

"While there are some great examples of leadership there are also some examples of ambivalence and that undermines change."

Ms May, managing director of Canberra-based The May Group, said many senior public servants were historically unaware of unconscious gender bias before detailed reviews of culture and processes.

"There is a far greater awareness of gender bias and stereotyping today but there is still a lot of work to be done," she said.

"In the public sector, gender bias varies between departments but one of the most significant areas relates to the management and support of part-time and flexible work arrangements.

"While many agencies have policies that support women and men with families and caring responsibilities, there are often penalties attached and that means assumptions are made about the availability and dedication of women.

"Assumptions are made about women being focused on their families and no longer on their careers and that's a big problem for women."

The strategy called on managers to promote flexible work arrangements more common in the private sector to ensure senior staff can manage work and family responsibilities.

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.

Ms May said gender bias was often neither malicious nor intentional and could be as subtle as communication or appearance.

"Women don't always have the opportunity to work on high profile jobs that are frequently obtained informally," she said.

"Men are much more likely to be part of those networks than women (…) or to have mentors who may ring them up and tell them there is an opportunity going."

The government 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".

To address the imbalance, the government has called on managers to prioritise the recruitment of women in areas such as science, IT and finance which have historically had few women.

Departments have also been told to strive for a 50-50 gender balance across the workforce with senior staff tasked with supervising and reporting on progress.