With more than a quarter of primary schools and a fifth of secondary schools lacking a permanent head, teachers’ unions say that the entire education system is at risk unless the Government helps to raise their numbers and gives them greater backing. Head teachers are blaming a daunting workload and long hours for problems with recruitment and say that, with a quarter of all teachers retiring in the next decade, the system is at breaking point.

In today’s report, the National Audit Office (NAO) authors say that heads are the “key to sustaining performance and improvement in any school”, but they also acknowledge that the numbers of “appropriately experienced people” applying for the posts are falling.

Ruth Kelly, the Education Secretary, told The Times last week that plans in the education White Paper for schools to collaborate would ease the shortage. But according to the NAO the problem is more complex. “In some places, head teachers have been asked to act as ‘executive head teachers’ and lead more than one school. This approach works in some cases and can help poorer schools by linking them with good schools, but it can also be risky given the challenges of school leadership and the importance of the personal presence of the leader.”

Mick Brookes, the general secretary of the National Association of Head Teachers, said that the lack of heads was one of the most important issues facing the Government, and that unless it was solved all other reforms would be virtually impossible.

He said that teachers were put off by becoming heads for several reasons: the high risk of taking the blame for a failing school; the extra workload to allow colleagues time for planning, preparation and assessment; and the minimal differential paid to heads as opposed to senior teachers. “For another £12.50 a week, who wants to take up that extra stress and responsiblity?” he said.

Edward Leigh, chairman of the Public Accounts Committee, called on the Government and local authorities to deal with the crisis. “More than one in five schools does not have a permanent head teacher, and the situation looks like it will get worse over the next five years,” he said. “The DfES [Department for Education and Skills] and local authorities must take urgent action.”

Last September, teachers’ unions warned the Govenrment that schools could soon be forced to share head teachers as many experience increasing difficulties in recruiting senior staff. Even though salaries reach six figures in some secondary schools, research by Education Data Surveys has shown that one fifth of schools that advertised for a new head had failed to appoint one this year.

Although the growing number of academies has pushed up the rates of pay for some secondary heads to more than £100,000, not even all those schools had filled vacancies. Church schools are also suffering as church attendance declines, and rural schools have been hit by the reluctance of families to move home. John Howson, director of Education Data Surveys, said: “Although it may sound ideal to work in a rural area, a partner might be twiddling their thumbs. And with more women becoming primary heads, there is a question of whose will be the dominant career.”

Last year, about £38 billion was spent on education and young people’s services, of which £840 million was directed at schools in England that were failing or at risk of doing so.

Although the NAO said that too many schools were failing children, they added that Ofsted, the education watchdog, and local education authorities could do more to help by carrying out more frequent inspections of schools at risk and giving greater support to head teachers.

Angela Hands, an NAO director, advised the watchdog to prioritise its inspections. “We’re saying Ofsted should look at the risk of individual schools and put their resources into those heading for trouble, rather than looking at all schools equally,” she said.

Ofsted, which recently lost its chief inspector, David Bell, who left to become the top civil servant at the DfES, said yesterday that it was seeking to implement the recommendations. “Ofsted is already planning to implement riskproportionate approaches to the inspection of schools and to follow up the progress of schools subject to special measures,” a spokesman said.

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