They fear the right to appoint teachers on religious grounds will be challenged by opponents using the Human Rights Act.

The National Secular Society says the exemptions bar tens of thousands of those with no and other faiths from jobs in church schools. It is taking legal advice.

But church groups say the freedom to appoint same-faith staff is essential if they are to maintain the religious ethos of their schools. Supporters credit their schools’ successes in academic performance tables to their ethos.

The exemptions, written into Section 60 of the School Standards and Framework Act 1998, allow schools to consider religious belief and practice in appointments, promotions and dismissals. Teachers appointed on this basis can be dismissed if conduct outside school is considered contrary to its ethos.

The churches say Education Secretary David Blunkett and his minister Baroness Blackstone have said that they will press for amendments to a new European Union employment directive on equal treatment, to ensure Section 60 is maintained.

“In the case of chools, the balance is between the right of a well-qualified teacher to seek employment in any school, and the right of a voluntary-aided church - or indeed Muslim, Jewish or Sikh - school to employ teaching staff who they believe would strengthen rather than weaken the religious ethos of their school,” said a joint statement issued by the Church of England, the Roman Catholic Church, and the Free Churches’ Council

But Keith Porteous Wood, general secretary of the National Secular Society, believes the exemptions - and their proposed extension to non-teaching staff - cannot be justified in an increasingly secular society where 30 per cent say they do not believe in God.

“Church schools are major employers with around 100,000 teachers, plus a substantial number of ancilliary staff. It is unreasonable for discrimination to be permitted on such a scale.

“It would be wholly unacceptable for non-teaching posts to be ring-fenced for believers. Many of these jobs are practically the only secure employment in isolated rural communities.”

A Department for Education and Employment spokesman said: “Schools are likely to argue successfully that a faith criterion can be objectively justified.”