There were 96 on Ofsted’s “special measures” list at the end of the Easter term, up two compared with the end of December. By contrast, the number of failing primaries fell from 180 to 156 over the same period.

The findings were published as it emerged that Unity City Academy in Middlesbrough had become the first of the Government’s flagship schools to be failed. The £18 million academy, sponsored by the construction company Amey, has been warned that it must go into special measures after a critical report by inspectors. It is already in rescue talks with the Department for Education and Skills (DfES) after overspending its budget by £1.5 million since replacing two failing comprehensives in 2002.

Unity City was among the first three academies to open but it moved into new purpose-built premises only last September. It has been criticised for expelling large numbers of pupils, while examination results have shown little improvement.

Ofsted’s judgment presents a challenge for Andrew Adonis, the architect of the academies programme. Tony Blair appointed his former education adviser as a Schools Minister last week to take charge of the £5 billion plan to open 200 academies by 2010.

There are 17 so far. The programme has proved highly controversial within the Labour Party, with critics opposed to the involvement of private-sector sponsors in the running of state schools.

Sponsors are given control of the governing body in return for a contribution of around £2 million to the £25 million cost of establishing each academy. Annual running costs are met by the taxpayer.

Mr Adonis, who also has responsibility for improving standards in London, believes that academies are a radical answer to the problem of entrenched failure in areas where local authorities are either unable or unwilling to raise standards.

However, MPs on the Labour-dominated Education and Skills Select Committee issued a critical report in March. They questioned why ministers were determined to spend so much on academies without any evidence so far that they were worth it.

Mr Adonis is said to be preparing a robust defence of academies in the DfES’s response to the committee. A DfES spokesman said that it was working with Unity City on a financial recovery plan and an educational action plan.

Schools placed in special measures by Ofsted face closure unless they can raise classroom standards within two years. Joe McCarthy, the chairman of the trust responsible for Unity City, said that “very difficult and painful decisions” were required to rescue the academy. New leadership has been appointed to deal with what he called a “legacy of financial, management and educational failings”.

Ten teachers and several support staff are set to be made redundant as part of a plan to end overspending. Teaching unions have threatened industrial action after the remaining teachers were told that they would have to work more hours for the same pay under new contracts. Officials at Ofsted declined to comment on the academy’s report until it has been published formally next month. A spokesman for Unity City also declined to comment.

Eddie Bradby, its former founding head, had described the academy as “a sign of hope, achievement and the future” for children in deprived areas of East Middlesbrough.

Its problems emerged as Ofsted’s first regional analysis of failing schools showed that the North East had the best record in the country. Only one primary and three secondary schools were in special measures in 2003-04, along with one special school and one pupil-referral unit, giving the North East a failure rate of just 0.6 per cent.

London has the highest proportion of failing schools. Eighteen secondary schools and 32 primaries are in special measures, a failure rate of 2.3 per cent of schools. The rate nationally is 1.5 per cent, with 332 schools on the failing list. www.timesonline.co.uk/education School and exam league tables

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