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.
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.
The figures were obtained through Freedom of Information requests
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.
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.”
Meg Hillier said some trusts “show a complete disregard for the use of public money”.
The Regional Schools Commissioner declared standards at Lilac Sky Schools Trust were unacceptably low.