Only one public service department out of 29 paid women more than men in 2015, according to figures from the State Services Commission (SSC).
The offices with the biggest divide between men and women were the Ministry of Defence and the Crown Law office, where men earned 39 percent more than women.
The Crown Law Office gender pay gap has risen 10 percent since 2008, while the gap at the Ministry of Defence increased 3 percent, the figures revealed.
The Ministry for Women was the only department where women were paid more - they earn about 37 percent more than men.
The gender pay gap, the difference between the average salary for women and men, excludes the pay of chief executives for individual departments.
The public service gender pay-gap average sits at 14 percent, and has done since 2010. This average includes chief executives.
Maori Development had a small margin of difference, with men paid 1 percent more than women; they were paid 2 percent more at the Corrections Department.
Government chief talent officer Andrew Hampton says the SSC is working to reduce gender pay gaps in the areas of leadership, improve the flexibility of working environment for parents and give equal pay for work of equal value.
"Improving the diversity of the public service leadership is an important focus for SSC, but will take time to achieve," he says.
"The gender makeup of public service leadership, while still not representative of New Zealand society, is moving in the right direction."
In the public service 40 percent of current or acting chief executives are women, the highest proportion there has ever been.
The proportion of women in senior leadership roles also increased from 39.6 percent in 2011 to 44.2 percent in 2015.
"The factors contributing to the gender pay gap are complex, which means that there are no easy solutions," says Mr Hampton.
He says the SSC is continuing to increase the amount of data analysis and reporting on diversity and equity in the public service.
Erin Polaczuk from the Public Service Association says the subject of equal pay needs to be tackled "once and for all".
"The public service workforce is the first in New Zealand to get an act providing for equal pay back in 1960, yet in 2016 we're still seeing women paid 14 percent less than men in that area," she says.
Ms Polaczuk says new policy needs to be implemented to eliminate the gap, and the Corrections Department almost reaching equality is an encouraging example.
She suggests public sector agencies reporting on the appointment of new staff by gender to make sure that men and women are being made appointed at the same rates of pay.
"Then throughout careers having salary scaled in collective agreements so everybody can see them and really transparent processes," she says.
Equal Employment Opportunities Commissioner Dr Jackie Blue says our publicly funded government departments should be leading by example.
"What we do know is that leadership by the chief executive makes the difference. Unless the system intentionally includes women, they will be unintentionally excluded."
She says the release of the figures needs to lead to "keeping women connected to the workplace while on parental leave, supporting women returning to work at the same level as they left at, flexible work practices and addressing unconscious bias in the workplace".
The Green Party says the figures show how much work needs to be done.
"Women shouldn't have to rely upon court action to get paid what they are worth. We should gave Government recognising the gender pay gap, and taking decisive actions to close it," says Green party co-leader Metiria Turei.
"It's time for the National Government to be bold and be fair," she says.
She suggests the Government set a target for reducing the gap year by year and then create policies to make that happen.
Figures from the State Services Commission are below:
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