Women working at Britain’s largest charity earn 21% less on average than men, gender pay gap figures reveal.

The Wellcome Trust, one of the world’s biggest funders of biomedical research, is the latest major institution to make public its record on gender and pay under new government rules.

Jeremy Farrar, director of the Wellcome Trust, said that the figures “inevitably make uncomfortable reading. An organisation has to face up to uncomfortable things and say ‘we’re not where we want to be and we want to change that.’”

The pay imbalance at Wellcome is linked to a disproportionate number of men in the top jobs, rather than men and women being paid different salaries for doing the same work, the charity said.

The figures showed that while women make up 64% of Wellcome’s workforce, they represent a minority in the top pay quartile and this imbalance was greatest at the very top tier of pay. The median difference in pay between men and women was 20.8%, above the national median of 18.1%. The most dramatic difference was in mean bonuses, where men earned 78.8% more than women on average.

This figure was strongly skewed by generous performance bonuses offered to senior members of the investments team, who manage Wellcome’s £20.9bn portfolio, all of whom were men.

Farrar said he was committed to transforming the gender balance at the charity, including having a gender-balanced executive leadership team, introducing gender bias training for staff and piloting new recruitment processes, such as looking beyond academia where most of the top posts are also dominated by men.

“We’re drawing on sectors that tend to be less diverse in the first place and if we draw from a limited pool we’re likely to perpetuate that,” said Farrar.

Farrar said that the charity was also revising the pay-band structure to help identify any cases of unequal pay and that there would be “no financial limit” set for correcting such inequalities if they emerged.

Government legislation now requires every organisation with more than 250 employees to publish the gender pay and bonus gaps and companies have until 5 April to submit their figures. Wellcome, which spent more than £1bn on biomedical research last year, is one of the first scientific institutions to make its figures public.

Most universities have yet to release their figures, although data published last year by the University and College Union identified a pay gap of 12% between male and female academic staff.

Prof Uta Frith, an eminent neuroscientist and head of equality and diversity at the Royal Society, said that while it is no surprise that many of the top jobs in science are held by men, putting a financial value on these disparities was acting as a “wake up call”. “That really does make people embarrassed,” she said. “People do feel, in a sense, valued by the amount of pay they get.”

Frith said the problem was not unique to Wellcome and that many institutions had failed to appoint senior women for reasons that were complex.

Farrar said that Wellcome has been too slow to improve diversity, but that the issue was now a priority. “Yes, it’s uncomfortable for many of us, but I do think there are moments when history can change and it is one to embrace and make the difference,” he said.

Prof Dame Athene Donald, master of Churchill College, Cambridge, said Wellcome ought to consider why there was a “gender segregation by grade” and whether the right people are being promoted for the right reasons. “Making diversity a priority is to be welcomed, but Wellcome need to be able to demonstrate that progress follows this promise in the years ahead,” she added.