Wakefield City Academies Trust (WCAT) was accused of transferring millions of pounds of schools’ savings into its own centralised account, during a Wakefield Council meeting in November.
Hemsworth MP Jon Trickett said he was "worried" that the government had not guaranteed the schools would get the money back.
On January 9, Mr Trickett submitted a written question to education ministers asking whether support and resources given to former WCAT schools when they are taken over by new academy trusts would include the return of the reserves.
Answering last week, Nadhim Zahawi, Parliamentary Under Secretary of State at the Department for Education said: "Wakefield City Academies Trust has chosen to take a trust-wide perspective of its finances, and is working with the Department for Education to ensure all 21 academies transfer to incoming trusts in a way that secures the financial future for each school and the education of their pupils.
"We are working with all of the schools and the preferred new trusts to determine appropriate support and resources, including funding, so that each of the schools has what is required to improve pupil outcomes.
"Our priority is to transfer the schools to trust that will be able to ensure every child receives an excellent education."
Following the response, Mr Trickett said: "I'm worried. The government haven't guaranteed the schools will get it back.
"Of course we all want a good education for our children, but it's absolutely not fair these schools have had to bail out a mismanaged trust ran by people with very little educational experience."
A meeting of Wakefield Council on November 22 last year, heard that three of the district's member schools could lose a total of more than £1.5m.
A motion debated by councillors said that Hemsworth Arts and Community Academy faces losing £436,000 of its reserves, Wakefield City Academy could lose nearly £800,000 and Heath View Primary £300,000.
WCAT made a shock announcement in September that it would cease running all 21 of its schools, including eight in the Wakefield district.
The trust’s board said it didn’t have the capacity to bring about rapid improvement in the academies.
But questions have also been raised over the trust’s financial management and allegations include reports of monies being “drained” from individual school accounts to pay off the debts of the parent organisation.
Speaking in parliament in November, education minister Nick Gibb said the trust will not be able to retain any of its reserves once it has formally been dissolved. And in a statement, a DfE spokesperson said: “A failing academy trust must never profit from the re-brokerage of its schools.”