The Department for Education spent more than £1.8 million paying off the deficits of academies before they were transferred to new sponsors last year, Tes can reveal.
The figure increases the amount of public spending known to be linked to rebrokering academies in 2016-17 to more than £8 million.
In September, the DfE published data showing it had paid £16 million in grant funding to move academies over the previous four years, including £6.3 million in 2016-17.
However, those figures excluded a number of costs connected to the rebrokering process, including deficit payments.
In response to a Tes freedom of information request, the DfE has now said it made total deficit payments worth £1,809,221 to five of the 59 academies that were rebrokered in 2016-17.
The Department for Education told Tes that trusts are "expected to pay this back", but was unable to give any details about the mechanism or timescales for this to be done.
Mary Bousted, joint general secretary of the NEU teaching union, accused the government of trying to hide the true costs of the academy programme.
She told Tes: “The key question is why the DfE continually tries to suppress information that should be in the public domain about the costs of the academy system.
“If you put schools out to the market, it is not surprising that multi-academy trusts who act in effect as buyers are refusing to take on schools with deficits.”
Three academies that received deficit payments before they were rebrokered belonged to the now-defunct Lilac Sky Schools Trust in Kent: Knockhall Academy (£699,547), Martello Grove Academy (£84,000) and Morehall Academy (£90,000).
The remaining deficit payments went to Callington Community College in Cornwall (£250,000) and the Totteridge Academy in Barnet (£685,674).
Asked why the DfE makes deficit payments to some academies and not others, Phil Reynolds, from accountancy firm Kreston Reeves, said that “ultimately, it does come down to negotiation and a bit of bargaining”.
He added: “Probably, there are trusts that did not realise that if they negotiated better, they could get a better deal.”
A spokesperson for the DfE said: “When an academy is transferred to a new trust the priority is to make sure all children get the best education possible. In the very rare cases where the ESFA provides extra funding, trusts are expected to pay this back."