In a study of the performance of 6000 academics, Canterbury Associate Professor Ann Brower set out to see if the gap could be explained by performance or age.
Dr Brower and her team found that even when women did just as well as men, they were far less likely to be promoted to professor or associate professor.
"Overall for all the universities, in all the fields, a man's odds of being ranked at the top are double the women's odds, with the same research performance score."
The difference in earnings over a lifetime could represent a large part of the price of a house, for example.
"So if you take me and the guy across the hall from me, over a lifetime, he'll earn 40 percent more of a house than I will."
Dr Brower and her co-author Alex James suggest possible explanations for their findings, including the idea that universities might demand more teaching activities from women than from men, without sufficiently rewarding the work.
The findings also show that current hiring practices will never close the gender gap in most academic fields. The study was published in the journal PLOS One.
New Zealand was the only country to measure this performance-based research data, and it is done every six years. The study looked at a decade of it from 2003-2012. While this was an international issue, Dr Brower said this data meant we had a world first in terms of analysis.
As the prime minister's chief science advisor, Juliet Gerrard holds arguably the top position in science in the country. When she took the role, she said she hoped she'd be able to inspire more women into science.
In her own experience, she had been fortunate, but added: "If I had $10 for each time someone has said that I achieved this promotion, or that position 'because I was a woman' I would be rich.
"It's tempting to say (with tongue in cheek) that this paper suggests that the reverse might more often be true - that some individuals are where they are today 'because they are a man'."
She said it was clear New Zealand had a long-standing problem, but this was the first time our national data set had been interrogated to back up - with hard numbers - what researchers knew from lived experience.
"The results are sadly not surprising - a mountain of anecdotes have suggested this significant pay gap is not explained by a difference in research performance and age."
Another member of the top brass is Wendy Larner, a provost - also known as chief academic - at Victoria University of Wellington.
She's also the second female president of the Royal Society of New Zealand, where she said concentrated efforts were being made to right the imbalance.
"We've got work to do. If we keep doing the same old, same old, as Ann and Alex show in their research, it'll take forever to change. We do need to do things differently."
A big part of her work as provost was to ensure the next generation of academics looked different and had different experiences to the ones she'd had over her career, she said.
"I have war stories, all women in universities have war stories. But I think now we're beginning to understand the more diverse we are, the better we are."
Association of Scientists president professor Troy Baisden said a lot of people in the research world like to assume colleagues were awarded on merit. But Baisden, also an environmental researcher at Waikato University, said studies like this one showed that this simply wasn't true.
"One reason we really worry about the results of this study is likely it's gender inequity in a way that builds up over a career.
"It's not just one decision where there's only a little difference, it's one grant, then the next grant, then the next promotion."
Dr Brower said the $400,000 figure was based on salary earnings over a lifetime - which didn't include grants, but those who ranked higher up the academic ladder were generally more likely to get research grants.
RNZ asked women in research what they would do with $400,000.
Some said they would put it towards post-doctoral studies, or a research project, or look at what keeps school kids engaged in science.
Some wanted to get it behind an environmental cause, donate to charity, or put it towards a mortgage.
One said she'd simply use it to "do something about the bloody imbalance".
Dr Brower plans to continue researching the issue.
This article was first published on Radio NZ.