Women working in schools run by multi-academy trusts experience some of the most stark gender pay gaps in the UK, Guardian analysis has found.

Of the companies to have filed figures on their gender pay gaps to date, almost half of the worst 50 are multi-academy trusts (MATs). All of the 23 trusts had gaps greater than 50%, meaning on average women working in the schools were paid 50p for every £1 earned by a man.

The figures come as part of mandatory gender pay reporting. Since 2017, companies with more than 250 employees are required to report their gender pay gap. The deadline for companies to report is 4 April and 4,350 companies out of an expected 10,000 had reported by 27 March.

What is gender pay gap reporting, and what does it mean? Read more

Nearly four in five MATs that have reported so far have a median pay gap worse than the national average of 17.9%. The median gap is the difference between the employee in the middle of the range of male wages and the middle employee in the range of female wages. Multi-academy trusts said the figures were a result of high numbers of women among their lowest earners, including teaching assistants and administrative roles, rather than the trust’s failure to promote women to the most senior positions.

Wimborne Academy Trust, which runs 11 schools in the south-west, reported a median gap of 68%, the biggest of any MAT. More than half of its leadership staff are women, including the chief executive, and three-quarters of the trust’s teachers are female.

In a statement to the Guardian, the trust said it was one of relatively few large MATs made up exclusively of first and middle schools. “Such schools usually have more support staff than teachers,” it said. “Women currently fulfil most of the support roles in the schools and a majority of our female employees are not teachers. Consequently the median paid woman in the trust is a teaching assistant.”

“Only 13% of the trust’s staff are male, and the majority of them are teachers. Therefore the median paid man in the trust is a teacher. The difference in pay between a teacher and teaching assistant accounts for the reported pay gap.”

Women tend to dominate the lowest paid jobs in MATs with a high gender pay gap. In the four MATs with the highest gaps, women made up at least nine in ten of the lowest paid. Just one of the 289 trusts to have reported so far had a 50:50 gender split among its lowest earners.

The National Education Union (NEU) said that, while some of the trusts with the highest median gender pay gaps had female CEOs, their median gender pay gaps would not fall until the gap between the salaries paid to the most senior staff and teacher and support staff was reduced.

MATs have been widely criticised for high executive pay. Analysis by Schools Week found that 23 trusts paid their chief executives more than £200,000 last year. Dan Moynihan, CEO of the 43-school Harris Federation, topped the list with a salary of £440,000. Last month academies minister Theodore Agnew wrote to chairs of academy trust boards asking them rein in CEO pay.

Rainham Mark Education Trust, which runs three schools in Kent, has a median hourly pay gap of 66%. Terry Whittaker, chair of the board of trustees at RMET, said that while at first glance the trust’s gender pay gap looked alarming, there were “proper and positive reasons for the apparent anomaly”.

“The trust currently comprises only three schools, one large secondary and two primary schools. The gender pay report is based on 252 employees of which 135 are support staff roles and 117 are teaching posts,” he said.

“Of our support staff 94% are part-time roles which traditionally have attracted more female employees looking for flexible, term-time roles with limited hours.”

Whittaker said that among teaching staff, women’s median hourly rate was 5% lower as a percentage of men’s pay, while among support staff it was 31% lower. He said that two of their three headteachers were female. “It would be an injustice to portray the trust as gender biased, in fact it would be inaccurate,” he said.

Kevin Courtney, the joint general secretary of the NEU, said the gender pay gap in many academy trusts was startling. “The NEU believes that the gender pay gap for teachers in academies is wider than for those in local authority schools,” he said.

“The Department for Education’s statistics show that while men and women classroom teachers alike are paid less in academies than in local authority schools, the loss is greater for women than men.”

He added that, while appointing women to senior positions in multi-academy trusts reduced the mean gender pay gap, the median gap would not go down until the gap between chief executive salaries and teacher and support staff salaries was reduced.

Jon Richards, the head of education at Unison, said women in lower paid jobs were often given tasks previously done by higher paid colleagues lost due to funding cuts. “Schools couldn’t function without support staff,” he said. “Academy chains must tackle the problem of low pay and as a society we must start valuing the support roles women tend to do if those gaps are ever to close.”

A government spokesperson said they were supporting schools to boost women’s progression in the workplace. “We have invested in a coaching and development programme for aspiring female teachers, in addition to £2m in equality and diversity hubs to share expertise and provide professional development for female teachers, as well as other teachers with protected characteristics,” they said.

Additional reporting by Leia Reid