The gender pay gap was greater in 21 departments than the labour market average of 11 per cent. Seven had a gap of more than 20 per cent, including the Treasury and the Department of the Prime Minister and Cabinet.
Only Corrections had no pay gap, and the Ministry of Women's Affairs had a pay gap in favour of women.
That's broadly in line with figures from the last Census of Women's Participation in 2012, which showed pay gaps of up to 42 per cent in some departments.
In contrast, the private sector appeared to be leading the way in closing the pay gap, Dr Blue said.
"Big businesses understand that if you increase your diversity and bring women through, you will actually improve your bottom line, so there's a strong business case for increasing diversity."
But smaller businesses often struggled with pay equality, despite being the backbone of the economy. Dr Blue plans to start work in that area by reaching out to business leaders and organisations.
"I'm sure that once they understand the business case, it's not a hard sell."
However, there was little appetite for a law change, Dr Blue said, despite a proposal three years ago by the Human Rights Commission to strengthen pay equality.
The outcome of a landmark equal pay court case, which is under appeal, could have a "huge impact", she said.
Lower Hutt caregiver Kristine Bartlett won a case in the Employment Court last year after arguing her $14.32 hourly pay rate was a case of gender discrimination under the Equal Pay Act. The ruling - which paves the way for pay equality in the female-dominated aged care sector - has been challenged in the Court of Appeal by Ms Bartlett's employer, Terranova Homes.
"If that case [finds in favour of Ms Bartlett], it's going to have a domino effect throughout the private sector, no question," Dr Blue said.
Her comments come as companies striving to close the gender pay gap can get recognition through a new award scheme aiming to raise awareness and promote change.
The YWCA Equal Pay Awards will acknowledge businesses which have implemented equal pay policies or are beginning to take steps towards closing the gap.
The awards will be backed by a range of resources, to be made available on the YWCA Auckland website, to help businesses work towards equal pay.
"One of the drivers around the Equal Pay Awards is to highlight this as an issue, but not just highlight it - to provide solutions for businesses," YWCA Auckland president Vanessa Ceelen said.
"There's not a lot of awareness that equal pay is still an issue in New Zealand, so certainly awareness is a huge part of this campaign. We want to support companies and help them help themselves."
Remuneration specialist Susan Doughty, who sits on the YWCA awards panel, is already starting to see changes in the private sector.
There was a good business case for pay equality, she said, and companies that understood the issue were able to attract and retain the right talent.
However, only a minority of businesses had started to grapple with pay equality seriously, and many were unaware of pay gaps within their organisation.
Pay differences were often due to an "unconscious bias" which could come into play during interviews and pay negotiations, Ms Doughty said.
Employers tended to be swayed by the negotiating styles of employees, which could differ between men and women.
Parental leave was another factor driving pay gaps within organisations, Ms Doughty said.
Women who took leave often missed out on a round of performance reviews, causing their pay to lag behind that of male colleagues with similar skills and performance.
The Human Rights Commission identified similar reasons for the pay gap, citing unequal starting salaries for the same job, female-dominated jobs being lower paid than male-dominated jobs, and women making up the majority among the lowest-paid staff.
Causes of pay inequality were "complex", a spokeswoman for Labour Minister Simon Bridges said, citing cultural and historical factors.
"The Government aims to reduce the gender pay gap by enforcing all relevant statutory requirements, such as non-discrimination in employment and requirements for equal pay," the spokeswoman said.
In response to the gender pay gap in the public sector, Deputy State Services Commissioner Sandi Beatie said it was her "expectation that public servants should be recruited and remunerated on merit".
The pay gap in the public service had been decreasing "for some time", with 2013 figures showing a 14.2 per cent pay gap compared with 16.1 per cent in 2006. Nine women held the top jobs in their respective government departments, including the roles of Secretary of Defence and chief executive of Te Puni Kokiri for the first time.
"The reality is the gender pay gap in the public service is heavily influenced by the relative pay rates in occupation groups where women are over-represented, such as clerical and administrative roles, contact centres and social, health and education workers," Ms Beatie said.
"The gender makeup of the public service is broadly representative of the wider population it serves. The percentage of women in senior leadership roles has been increasing since 2009, and 59.8 per cent of public servants are women."
The Ministry of Defence was highlighted in the 2012 report as having the largest pay gap, at 42 per cent. But it was its response to the report's authors that was "of most concern" to the commission.
"The ministry has no areas of concern regarding gender pay and employment equity in the ministry," it told the commission.
Company makes sure parents kept in pay and promotion loop
Many new mums give up the chance for a pay rise while they take parental leave.
Louisa Buchanan not only got a salary increase but she also got a sought-after promotion just two months after returning to work.
The 34-year-old Aucklander is a human relations consultant for Coca-Cola Amatil, which has committed to gender pay equality for its staff.
When she took time off to care for her daughter Ruby, now 2, she was able to take advantage of policies that ensure employees on parental leave don't fall behind their colleagues.
Parents' salaries are reviewed while they are on leave, which ensures they don't miss out on a chance for a pay rise.
Ms Buchanan, who has been with the company for seven years in various roles, said that was important.
"I worked my way up and the big thing for me was, when I went on maternity leave, I didn't want to be disadvantaged and come back on the same salary." Ms Buchanan took 10 months' leave before easing back into her role with a two-month flexible working arrangement. Then, only two months after she returned to work full-time, she got a promotion.
"Because I had a good two years of recruitment under my belt, I was really looking for a different challenge, and it was probably only two months after I returned from maternity leave that I was promoted," she said.
"It was a very short time - there was no sort of coming back to work and second-guessing people. They really supported me through that process."
Ms Buchanan is enthusiastic about Coca-Cola's other policies aimed at new parents, including training and education opportunities, free healthcare for parents and their children, and six weeks of paid parental leave, in addition to the standard 14 weeks of paid leave.
She wouldn't be with the company if she felt disadvantaged, she said - although she admitted she took it for granted.
"But then I've also gone out and made sure that we're at the cutting edge of benefits for returning-to-work parents, and there is a real gap in terms of people being disadvantaged in the market. For me personally, it was awesome, it was amazing."
Work to be done
Some areas where pay gaps remain
• Accountancy: 26% pay gap.
• PR/communications: In the 30+ years' experience bracket, men earned an average $16,885 more than women.
• Health: 18 of 20 District Health Boards provided information. 12 indicated they had pay gaps of 13% and below, two had pay gaps between 20% and 30%, and four had gender pay gaps between 30% and 40%.
• Science: Women with a BSc earn on average $30,000 less than men with the degree and this difference continues at higher levels.
Source: Human Rights Commission.
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• Visit tinyurl.com/nzhwomencensus to read the Human Rights Commission report on gender participation