New Zealand's female medical specialists are earning on average 12.5 per cent less than their male counterparts, despite being the same age with the same experience.

And the gap only widens for women who leave to have children; the more children they have the bigger the gap gets, new research shows.

Dr Isabelle Sin, a Senior Fellow at Motu Economic and Public Policy Research, is the lead author of a report commissioned by the Association of Salaried Medical Specialists.

"We compared doctors of the same age, in the same specialty, who work the same number of hours each week and found women earn substantially less than men," Sin said.

"We tried improving our controls for experience and throwing in all the other personal and job characteristics that might matter, but we just couldn't explain most of the gender pay gap."

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For specialists without children, there is a smaller but still statistically significant gender wage gap of 9 per cent. That wage gap widens to 14 per cent for those with one child and to 17 per cent for those with two or more children, she said.

The size of the DHB also made a difference.

"DHBs that employ fewer than 200 doctors have the largest wage gaps, averaging 19 per cent. DHBs employing 500 or more doctors have smaller average wage gaps of 12 per cent. DHBs of intermediate size have the smallest average wage gaps of 9 per cent," she said.

Hourly earnings were "relatively stable" for men and women over 45, which suggested that beyond a certain level of seniority, hourly wages were determined almost entirely by factors other than experience, she said.

The research also found a substantial gender pay gap among new immigrants, which was consistent with male specialists disproportionately receiving additional payments beyond the contracted minimum.

The research team used data from the 2013 Census on hours worked with administrative earnings data to calculate hourly earnings for the population of doctors employed by DHBs in March of that year.

The report states the country's medical profession was not typical of other high-skill professions.

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Unionisation among public system doctors was high, and the pay and conditions negotiated by their union, the Association of Salaried Medical Specialists (ASMS), in their Multi Employer Collective Agreement (MECA) with the 20 District Health Boards.

Among conditions of the MECA are salary steps that specify minimum pay at each level of experience, and the stipulation that, except in exceptional circumstances, specialists move up a salary step with each year of experience until they reach the highest step.

That included those who were on parental leave for up to a year.

It was thought that condition might be expected to limit the potential for a gender pay gap.

Researchers had a "95 per cent confidence interval" for its pay gap estimate of between 9.9 per cent to 15.1 per cent, so they could "convincingly reject equal pay of medical specialists by gender".

They also researched Resident Medical Officers (RMOs) and found a "statistically significant gender wage gap of 11.0 percent".

"The gender wage gap is larger at older ages, for those who work fewer hours for a DHB each week, and between men and women who are parents.

"These differences cannot be explained by women entering the profession at older ages or taking more gaps in their employment.

"Our findings suggest men may be placed on a higher starting step when they begin work as specialists, men who move between DHB employers mid-career may be placed on higher salary steps than equally experienced women, or men may disproportionately receive additional payments beyond the MECA minimum."

The country's medical profession was historically male, and remained dominated by men.

However, researchers discovered it was in the process of change as women now outnumbered men among doctors aged under 30 employed in the public health system.

However, female doctors still faced greater challenges including they're more likely to get bullied at work, have greater work-life conflicts, are expected to be more empathetic, approachable, and communicative, yet receive less support in their jobs and are viewed more negatively by patients, peers and medical students.

They were also less likely to be correctly identified as doctors, both by patients and other medical staff, which could increase the pressure they felt to perform.

The report stated international evidence was mixed as to whether male or female doctors were more likely to experience burnout however, research into burnout rates of New Zealand hospital-based specialists found a significantly higher rate of burnout in females.