Church schools outperform their secular neighbours because they select their pupils, not because they have a religious ethos, the official admissions body has said.
It turned down a request from Southborough boys secondary modern in Surrey to become a Church of England school. Southborough said the new Christian ethos would raise standards.
But the Office of the Schools Adjudicator said that the only reason faith schools beat their secular neighbours was because of "their practice of selection from church-going families".
In a report released this month, Alan Parker, the schools adjudicator, rejected the application and said: "The argument advanced by the school that a religious ethos will have a beneficial academic effect is speculative."
The Diocese of Southwark, which supported the school's bid, has written to the adjudicator asking for further evidence to support his view that church schools select.
Mr Parker's comments come as a new government study into the reasons for the success of faith schools begins.
Latest figures show 51 per cent of CofE pupils left school with five good GCSEs compared to 42 per cent of children at non-denominational schools.
Canon John Hall, the Church of England's chief education officer, denied success was achieved because schools skewed their intake. He told the Association of Anglican Secondary School Heads' annual conference in Cumbria: "There are tremendous examples of schools where it is clear that's not true. Much of the value schools add is down to them understanding the importance of pupils' spiritual and moral development."
He said it was hoped that the pound;25,000 study commissioned jointly by the church and the Department for Education and Skills would set the record straight. The research will analyse value-added scores of pupils at CofE schools and look for reasons why some schools score higher than others.
But one of the last similar research projects, in 2000, found little evidence that faith schools were better at improving the results of low-achieving children.
Dr Sandie Schagen, principal research officer at the National Foundation for Educational Research, which was behind the study, said: "Church schools do very well, but that's because they have the best pupils.
"Parents have the perception that they are good schools and they will fight to get their children into them."
Marilyn Mason, education officer at the British Humanist Association, who objected to the Southborough proposals, said: "A church school's ethos and curriculum is not going to appeal to everyone. A Christian policy on worship in schools is going to put a lot of people off - that is an implicit selection policy."
A study last year found one in six church schools still interviews prospective pupils - a practice due to be banned by September 2005.
The London School of Economics found church and foundation schools were 25 times more likely to select pupils who will boost their league-table ratings.
Krysia Butwilowska, head of St Luke's C of E school in Portsmouth, which has seen the number of pupils achieving top results soar in recent years, said it was insulting to attribute the rise to selection.