The findings - which last night drew a fierce response from the Church of England - will reignite the debate about the role of religion in the education system and come as the government attempts to reassure critics that faith schools do not favour the selection of middle-class, white pupils.

Rebecca Allen, of the Institute of Education, University of London, and Professor Anne West, Professor of Education Policy at the London School of Economics, studied the intake of faith schools across the capital using an extensive 'pupil-level' database compiled by the Department for Children, Schools and Families. Although the majority of faith schools were established to educate the poor, the two academics said it appeared many had moved away from their original remit. While observing there are exceptions, the researchers found religious secondary schools in London educate a smaller proportion of pupils eligible for free school meals than non-religious schools and that their intakes are 'significantly more affluent' than the neighbourhoods in which they are located.

Their research showed 17 per cent of pupils at faith schools are eligible for free school meals compared with 25 per cent at non-religious schools. Faith schools educate just under 20 per cent of lowest-ability pupils compared with 31 per cent of non-religious schools. Faith schools also educate a greater proportion of the pupils who score highest before arriving in secondary education.

'This research poses important questions for policymakers,' West said. 'My concern is that the [current system] is giving schools an incentive to select pupils who are easier to teach.'

Although faith schools tend to be located in less affluent inner-city areas, the research found pupils from ethnic minorities that are over-represented in such locations are largely absent. Just one per cent of Pakistani and Bangladeshi pupils are educated in faith schools, the researchers claim.

The claims are likely to be seized upon by critics of faith schools. Last year research revealed many headteachers were deeply concerned about the effect of the schools on the education system. In one poll almost half felt there should be fewer or no faith schools.

'This research shows once and for all that so-called faith schools are simply private schools on the rates for those who know how to play the system,' said Terry Sanderson, the president of the National Secular Society.

Yesterday, ministers strongly denied the government was planning more faith schools. 'The government has no policy to increase the number,' said Ed Balls, secretary of state for Children, Schools and Families. 'It is up to local communities to decide the kind of schools they want.'

A spokesman for the Church of England said the research did not reflect the true picture across the country as a whole. 'The LSE study focuses purely on London, which has a very different demographic to the rest of the country,' the spokesman said. 'The Church always has, and always will be, committed to serving the communities within which our schools are located.'