Financial failings, including the disappearance of tens of thousands of pounds, false invoicing, and questionable staff appointments and payments have been uncovered during a top-level probe into the running of a flagship free school in Bradford.

Department for Education auditors were called in to examine the books of the Kings Science Academy in Lidget Green after concerns were raised by a whistleblower about the way it was being run since it opened in September 2011.

The investigators found a series of major failings in the school’s financial controls which has led to almost £77,000 of £183,000 Government start-up cash still being unaccounted for and now having to be paid back.

The probe also found the principal Sajid Hussain Raza had employed members of his family at the school, including his wife and sister as teachers on a combined salary of more than £49,000, and his father as a minibus driver on a wage of £6,950, all during the year ending August 31, 2012.

There had been a failure to appoint a suitable finance director; a failure to appoint a clerk to the governing body, and a failure to follow correct governance procedures or implement proper financial controls.

The auditors found incorrect payments had been made to the principal and no explanation could be given as to why one governor was paid £5,612 in expenses.

And the school was found to have paid for the refurbishment of a property owned by a company of which Mr Raza is a director and his father a trustee.

A report published yesterday by the DfE reveals that the investigation took place early this year and the school was issued with a warning notice in May.

A DfE spokesman said: “We found serious failings in financial management at the Kings Science Academy (KSA). We informed the police who decided no further action was necessary.

“We required KSA to address these failings urgently. A plan is in place to recover funds and the school is undertaking its own investigation. Any necessary disciplinary action is a matter for the school.”

The National Union Teachers has now demanded answers from the Government how the situation it condemned as a “disgrace” was able to arise and further criticised the free schools programme.

The union’s general secretary Christine Blower said last night: “It is now apparent that the DfE has been sitting on the report detailing financial irregularities at the Kings Science Academy since May and only released it late today once it became clear that the NUT had released to the press its own document outlining financial irregularities at the school.

“The catalogue of irregularities and what frankly points to fraud in the management of the school’s finances acknowledged in the DfE’s investigation report is a disgrace.

“This makes it very clear that the DfE lacks the proper procedures to manage and oversee its free schools programme. The audit investigation team deemed that the situation was so serious as to warrant investigation by the police.

“Problems around good governance, financial probity and standards of education are emerging in increasing numbers of free schools. The Government cannot continue to claim that these are isolated cases.”

Ian Murch, the union’s Bradford spokesman, added: “We have got some big concerns about the way in which this school has been set up and the way in which it is operating.”

The DfE last night insisted that free schools and academies are subject to stricter financial scrutiny than maintained schools.

Its spokesman said: “Unlike maintained schools, academies must have their accounts externally audited. Unfortunately no system of financial accountability for any school can guarantee it will prevent all wrongdoing.

“However, we take swift action when concerns are raised – academies and free schools cannot hide from their financial responsibilities and are held to account for their actions.”

Councillor Ralph Berry, the executive member for children and young people’s services at Bradford Council, said the local authority was now helping the school on “governance issues” at the request of its governors and also criticised Government policy.

He said: “My fire is firmly aimed at the DfE and overall policy. The Government’s own policy has provided an inadequate framework to make sure these projects are managed by normal rules.”

When the Telegraph & Argus contacted the school yesterday we were told by a woman who answered the phone that Mr Raza and the school had broken up for October half-term and she would try to contact him. He remained unavailable for comment last night.

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