A number of academy bosses saw their salaries rise last year, with some taking home significantly more than the Prime Minister.
In a few cases, chiefs were handed pay rises worth several thousand pounds, annual accounts show.
The statements also show that three academy trusts were victims of fraud in 2015/16, with some funds still outstanding.
The highest individual earner was Sir Dan Moynihan, chief executive of the Harris Federation, according to an analysis of 20 academy trust accounts conducted by the Times Educational Supplement (TES).
He saw his pay packet rise from £395,000-£400,000 in 2014/15 to £420,000 - £425,000 - up a minimum of £20,000.
A Harris Federation spokeswoman told the Press Association that the trust had transformed some of London's most challenging schools, and all 30 of its academies that have been inspected by Ofsted had been rated as good or outstanding.
The spokeswoman said: "With 41 academies in total, we have maintained our success as we have grown. Harris has been recognised as a top performer by researchers at the DfE, Sutton Trust and Education Policy Institute - as well as Watchsted and PwC.
"Our Board recognises that leadership is among the key drivers of our success, so leaders throughout our federation are rewarded for their contribution."
The analysis shows that Ian Comfort, former chief executive of the Academies Enterprise Trust (AET) - which runs 66 schools across England, was paid £236,000 in the last academic year, up from £225,000.
Toby Salt, chief executive of Ormiston Academies Trust - who will soon move to head up the AQA exam board, took home £205,001-£210,000 in 2015/16, up from £200,001-£205,000 in 2014.15, while Alan Yellup, who served as chief executive of Wakefield City Academies Trust until last May, had a salary of £180,001-£190,000 compared to £160,001-£165,000 the year before.
In comparison, Theresa May earns around £150,000
The TES analysis also found that 16 workers at the Oasis academy chain earned at least £100,001 in 2015/16 - up from 10 employees in 2014/15, and at Ark Schools, five staff members earned more than £150,000 - up from three the previous year.
At Outwood Grange Academies Trust, the highest paid employee, chief executive Sir Michael Wilkins, saw his salary drop from £200,001-£205,000 to £170,001-£175,000.
This is because he reduced his hours, the trust told the TES.
United Learning Trust was one of the chains affected by fraud, the analysis showed.
Its annual accounts reveal that it paid a "valid, appropriately approved" construction invoice for £240,800 into a fraudulent bank account, adding that internal controls were "insufficient to detect this type of third party attack".
The trust recovered £220,883 and is still working with others to recoup £19,917.
A spokesman said: "As a result of this incident, we have since conducted a full review of our internal processes and have tightened our internal controls.
"There have, in the past, been several other attempts to defraud the group all of which have been identified and prevented with no losses incurred".
Bright Futures Educational Trust (BFET) was defrauded out of £15,999 after paying a "valid, appropriately approved" invoice for the amount into a fraudulent account.
A spokeswoman said: "We have recovered most of the monies and are working to recover the remaining £5,297 - additional controls have been implemented to prevent re-occurrence."
And "fraudulent correspondence" for £10,734 was received by the Griffin Schools trust, requiring a change of bank details for a supplier.
As a result, payment was made to an incorrect account. The money was recovered in full.