The Ministry for Women - which aims to eliminate the gender pay gap - has defended paying its male staff 6 percent more than its female staff.

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Minister for Women Julie Anne Genter was questioned by MPs about the disparity at a Parliamentary select committee this morning.

Photo: RNZ / Rebekah Parsons-King

Ms Genter said the figures were skewed by the agency's small size.

"Obviously, the smaller the organisation, the more [the pay gap] bounces around with just one or two changes in roles," she told MPs. "What we want to see is balance."

As of 30 June 2018, the Ministry's gender pay gap was 6 percent in favour of men. At the time, it employed 21 full-time staff and eight part-timers.

The year before, the disparity was 5.6 percent in favour of women.

Ministry chief executive Renee Graham said most of the agency's staff were women, but more men had recently come on board.

"We've got six men in our agency now which is the highest [number ever]," she said. "What that does is flick your gender pay gap."

National MP Louise Upston asked how the agency planned to address the disparity, noting that it must be "frustrating".

Ms Graham said the Ministry had a "gender pay gap action plan" like all government agencies.

The Ministry was also one of seven agencies which were trialling "flexible-work-by-default" approaches, she said.

The State Services Commission late last year announced that the average gender pay gap in the public service was 12.2 percent.

The Ministry for Women's workforce data was not included in that calculation because of its small size, but the agency independently released its own pay gap information.

The government has committed to eliminating the gender pay gap within the public service by the end of 2020.