New concerns have been raised over the pay handed to academy school bosses after it emerged that almost 1,000 academy trusts paid a six-figure salary to at least one staff member last year.

A total of 988 trusts, the not-for-profit charities that oversee academy schools, had at least one person on £100,000 or more in 2017-18, with 146 paying £150,000 or more to at least one employee.

The proportion of trusts paying £150,000-plus salaries has risen by 20% in a year, with a 7.6% rise among those with at least one person above £100,000. The rise came despite an increase in the number of academy trusts in deficit, from 5.9 to 6.4%.

The official figures, released last week, will fuel criticisms of the government’s academies programme. There have already been rows over schools using their independence to pay big sums to senior management. It comes amid huge concern over the financial pressures on classrooms.

Academies are not part of nationally set pay structures so trusts are left free to set remuneration as they see fit. Most of the best-paid leaders in English schools are now trust chief executives, running groups of academies. Since last year ministers have written to 213 trusts with at least one person on £100,000 or more asking for justification. However, only 50 trusts had reduced remuneration.

Outside the academies system, it is relatively rare for a school leader to reach six figures. The top of the national pay range for headteachers, which applies to non-academy schools, was £116,738. This would be paid to a very small minority of leaders running large local authority secondary schools in London.

One of the trusts to pay out a £150,000-plus salary was the Education Fellowship Trust based in Kettering, Northamptonshire. Last year it was in the process of giving up all its schools after it collapsed amid reported financial problems and concerns from Ofsted about low standards.

The figures have been a cause of concern to teaching unions, which warned that the oversight of academies was breaking down. Kevin Courtney, joint general secretary of the National Education Union, said they showed the government was “failing to tackle problems that are endemic to the academies sector”.

“This is not just poor management by government,” he said. “It is a sign that the system itself cannot be run efficiently and in a way that is transparent and accountable to parents.

“The DfE cannot gloss over the fact that the academies project is becoming increasingly unstable and impossible to manage. Systemic problems are driving up the costs of administration and allowing money to be siphoned off into excessive salaries for unaccountable academy leaders. It is now time to abandon this failed project and return schools to a stable, democratically accountable and supportive local authority framework.”

A Department for Education spokesperson said: “Academies are helping to drive up standards in schools across the country. The salaries of top executives in trusts should be a reflection of responsibilities and the performance of schools under their control.

“We recently published guidance on setting pay for top executives to help all trusts set salaries at a level that is publicly justifiable.

“Over the last 18 months the government has committed to curbing excessive executive pay in a tiny minority of trusts to ensure it is fair and proportionate to the task in hand, and this approach is already yielding positive results.”