Nearly half of academy trusts have paid millions of poundsin public money towards the private businesses of directors, trustees and their relatives, Whitehall’s spending watchdog has disclosed.

The National Audit Office says 976 academy trusts – 43% of those examined – disclosed “related party transactions” in 2013 worth an estimated £71m. Almost £9m of this money posed a risk to public money, it added. Margaret Hodge, the chair of the public accounts committee which will question education officials about the figures, said the Education Funding Agency (EFA), which oversees the finances of academies, needed to get a grip of these “dubious” relationships.

“Related party transactions are a big issue … I am very concerned that the agency’s reliance on whistleblowers and ad hoc reports means that many more questionable business relationships could exist and have gone unchallenged, putting public money at risk.

“Given its track record, I have little confidence that the agency will know if academies are complying with its new guidance on dealing with related party transactions,” she said.

The new figures have emerged after the EFA reviewed the financial statements of all academy trusts to identify contentious transactions such as related party transactions – defined as “a transfer of assets or liabilities or the performance of services by, to, or for a related party”.

The auditors’ report found that in 2012-13, out of a total of 2,256 academy trust financial statements that the agency reviewed, 976 disclosed “related party transactions”.

Of academies’ £11,467m expenditure that year, an estimated £71m was recorded as “related party transactions”. Of these, £8.6m was assessed by the agency as posing a risk to value for money and required further work.

The report was sparked by inquiries into alleged irregularities and potential conflicts of interest at the Durand academy in south London.

The school has become a favourite among traditionalists because it offers a public school boarding education to inner-city children, many of whom are from minority ethnic backgrounds.

Auditors examined the EFA’s oversight of Durand and identified possible conflicts of interest for the purchase of legal services from a company where a Durand governor was the company secretary.

The structures of the Durand Academy Trust and related organisations were so complex and involved many of the same officers, the auditors found, resulting in a large number of conflicts of interests.

Hodge said: “It feels just wrong that individuals sitting on the board of the Durand Academy Trust could set up such a complex web of organisations and companies some of which are selling goods and services to the academy. It’s not at all clear if individuals within the trust were improperly benefiting from these companies.”

Earlier this year, the Guardian disclosed that payments to academy chains have been made for a wide range of services including consultancy fees, curriculums, IT advice and equipment, travel, expenses and legal advice.

The report also disclosed that Sir Greg Martin, executive head of Durand, saw his wage packet, including pension contributions, increase to a total of £229,138 in 2013.

It added that the EFA was planning to undertake a review of academy heads’ salaries, but had yet to finalise the scope of this.

A spokesperson for the Durand trust said the arrangements the NAO looked into had delivered significant benefits for pupils and were established in good faith.

“We agreed with the EFA to review our structures and governance six months ago, so that we remain in line with the very latest edition of the Academies Financial Handbook. As the NAO’s report confirms on Thursday, many of the changes we instigated back then are already complete, or under way and nearing completion,” the spokesperson said.

• This article was amended on 13 November 2014. An earlier version referred to 971 academy trusts where it should have said 976; the incorrect figure came from a National Audit Office statement, the wrong version of which was sent to us.