The Government does not have a clear view of how taxpayers’ money is being spent on its flagship free schools and is too reliant on whistleblowers to expose problems, a cross-party group of MPs has warned.

In a new report, the Commons Public Accounts Committee suggested that financial management and governance in some of these new schools, including the Kings Science Academy in Bradford, was not up to scratch.

It also expressed concerns that there had been no bids to open primary free schools in areas that have a high or severe need for places.

The report analyses the success and value for money of the free schools programme and says that the Government has made “clear progress” on the scheme – which is a key part of its education policy – by opening new schools quickly.

But it adds that the measures put in place for checking how these schools are run and whether money is being spent properly are not good enough.

Fewer than half of free schools submitted their financial accounts for 2011/12, to the Education Funding Agency (EFA), as they are required to, on time, it says.

The MPs highlighted recent governance and management issues at the the Kings Science Academy in Lidget Green.

It suggested that the Department for Education (DfE) and EFA’s processes for overseeing free schools “are not yet working effectively to ensure that public money is used for the proper purpose”.

The report goes on to say that the DfE and the EFA “seem overly reliant on whistleblowers when problems should have been identified through their own audit and review processes”.

PAC chairman Margaret Hodge said: “Recent high-profile failures demonstrate that the DfE and the EFA’s oversight arrangements for free schools are not yet working effectively to ensure that public money is used properly.”

She added: “The department and agency have set up an approach to oversight which emphasises schools’ autonomy, but standards of financial management and governance in some free schools are clearly not up to scratch.

“The agency relies on high levels of compliance by schools, yet fewer than half of free schools submitted their required financial returns for 2011/12 to the Agency on time.”

Miss Hodge said that the Government needed to improve its systems for scrutinising free schools.

In response, a DfE spokesman said: “As the PAC has recognised we have made significant progress in implementing free schools, which are driving up educational standards and giving pupils from all backgrounds the chance to achieve academic excellence.”