Debts run up by 113 academy trusts in England amount to almost £25m, figures obtained by the BBC suggest.
The numbers raise “serious concerns about the accountability” of the system, said Meg Hillier, chairwoman of the Commons Public Accounts Committee.
More than half of England’s secondary schools are run by self-governing academy trusts.
The government said financial oversight of academies was “more robust than in council-run schools”.
The DfE’s Education Funding Agency investigated one academy trust, Lilac Sky Schools, over its financial governance.
It runs nine primary schools in Kent and East Sussex. The most recent accounts show a deficit of £665,972.
‘Threatened with closure’
And last year one of its schools was threatened with closure because of poor academic performance.
In the year 2013-14, Lilac Sky Schools Trust (LSST) paid £800,000 to outside companies set up by co-founders Trevor Averre Beeson and his wife Jane Fielding.
The Education Funding Agency has since ordered that payments to these companies cease.
Ms Fielding, who was an LSST managing director, was also paid a salary totalling £200,000 over the years 2014 and 2015.
Mr Averre Beeson’s daughter, Victoria Rezaie, who was employed by the trust as a principal, received a salary of £63,298.
Another daughter, Samantha Busch, was employed by LSST for £16,593.
In November, the Regional Schools Commissioner’s office for London and south-east England issued a pre-termination warning notice to the trust over “unacceptably low” standards at LSST’s Marshlands academy in East Sussex.
The trust now has to hand nine schools to other trusts before the end of the year.
‘Results, results, results’
“At first it looked like this would be a good thing,” said the parent of a child at a Lilac Sky School.
“Parents were impressed. Very soon the school was flooded with ‘Lilac Sky’ managers, and ‘outstanding achievement coaches’, of course all wearing something lilac.
“But soon afterwards problems began to emerge with the departure of experienced staff, and their replacement by less experienced teachers.”
The parent added: “All the time the pressure was on results, results, results and that meant the less able got left behind.
“Many of the non-core, fun things that are an everyday part of most primary schools were cut – swimming lessons, music lessons, school trips.
“However money was made available to send children who were soon to sit Sats on Sats booster courses at other Lilac Sky schools in the county.
“As far as I’m concerned this was all about business and making money and little to do with educating children.”
Trevor Averre Beeson responded by saying: “We are extremely proud of Lilac Sky Schools Limited.
“Since 2009 we have run over 17 schools and worked in hundreds more, nine of which were removed from special measures in very quick time, four improved significantly and four new schools opened to Ofsted’s satisfaction.
“The deficit for the trust in 2015 was due to costs associated with setting up four new primary academies. The individual schools themselves were all in surplus.”
He said that his wife and daughter had been employed by the trust “because they were already successful teachers”.
And he added: “We voluntarily decided that our companies should stop providing services to the trust when I also resigned as CEO and trustee in early 2015.”
The scale of the deficits accumulated by academy trusts was revealed in a Freedom Of Information request obtained by BBC 5 live Investigates.
Perry Beeches, which runs five schools in Birmingham, had a deficit of £2.1m in the last financial year.
Former chief executive Liam Nolan, who quit earlier this year, was criticised for receiving £80,000 a year as a consultant to the trust in addition to his £120,000 salary as head teacher.
Mr Nolan declined to comment.
Meg Hillier said some trusts “show a complete disregard for the use of public money”.
She added: “This is not their money they are spending, it’s our money. There are rules about how this is done for a good reason.
“This is not about whether the academy system is good or bad for education, it’s about how taxpayers’ money is spent.
“These figures raise serious concerns about the transparency and accountability of the system.”
In a statement, the Department for Education said: “All academies operate under a strict system of financial oversight and accountability, more robust than in council-run schools. Where issues are identified we can and do take direct action.
“All academy trusts must balance their budgets from each academic year to the next. Only a tiny number (4%) of academy trusts reported a deficit at the end of the academic year 2014-15 and we continue to monitor them very closely.”
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