There are approximately 114,000 teachers working in faith schools today and their number is expected to increase. Tony Blair, the Prime Minister, has praised their “strong ethos and values” and approved 100 new faith schools since Labour came to power.

Thousands of new school places will be created over the next few years as more community schools are handed over to the church, private minority-faith schools opt into the state sector and faith groups such as the United Learning Trust and the Emmanuel Schools Foundation fund city academies.

Supporters praise faith schools’ high standards, pointing out that two-thirds of the country’s top-performing primaries are faith based.

Critics accuse them of cherry-picking: most faith schools have significantly fewer children on free school meals than others. But opposition runs deeper than a mere squabble over league tables.

Last month, the Association of Teachers and Lecturers union took the unusual step of releasing a statement denouncing faith schools, saying they should lose government funding unless they “embraced diversity”.

Research has also highlighted the schools’ divisive influence. A report by the Institute of Public Policy Research found that faith schools that controlled their own admissions criteria were 10 times more likely to be unrepresentative of their surrounding area.

Critics fear the schools will exacerbate religious tension, and concerns about religious dress in the classroom have been voiced.

In this context, organisations such as the British Humanist Association and the National Secular Society have campaigned for a French or American-style secular education system, confining religion to private life.

But the issue divides the profession. Faith schools are fiercely protective of their “distinctive” character and do not want to see it watered down by an obligation to admit 25 per cent of children from other faiths, as proposed last year.

The plans, mooted by Alan Johnson, the Education Secretary, were quickly steamrollered by faith leaders.

The Muslim Council of Great Britain said England did not have enough Muslim schools to cater for existing demand, while the Christian churches touted their pluralist credentials. The Catholic church claimed its schools included on average 30 per cent of children from other faiths. And the Church of England introduced a voluntary 25 per cent quota, although it is up to individual governing bodies to enforce it.

The issue of whether faith schools promote diversity is a sticky one.

International research shows no evidence that they foster terrorism. But a Home Office report into the Bradford riots of 2001 criticised faith schools for institutionalising segregation and even some Anglican clerics are speaking out. “We should not have more faith schools at a time when we should be unifying, not separating,” the Revd Richard Bentley, vicar of Petersham, told The TES.

But faith schools are quick to fight back. Clare Sealy, the head of St Matthias CofE school in Tower Hamlets, east London, points out that less than a quarter of her intake is white British and two-thirds are Muslim.

Faith leaders argue that religious schools foster an ethos of care and equality that would be the envy of some gang-ridden inner-city community schools. But the point remains that almost all voluntary-aided religious schools discriminate on grounds of faith and can even stipulate the religious preferences of their teachers.

“If your best local school is a faith school and they don’t want you, what are you supposed to do?” one parent said. The conundrum doesn’t appear to apply to politicians: both David Cameron and Tony Blair have secured their children places at high-performing church schools.

There are also concerns over whether faith schools, many of which boast a strong spiritual approach to the curriculum, are mixing fact and faith.

Last year, a teacher at Sir Peter Vardy’s Emmanuel college in Gateshead was forced to resign from the creationist group Truth in Science over fears he was teaching the controversial theory in science lessons. The school denied the charges.

But questions about practices in faith schools keep cropping up. This year, the King Fahd academy in Acton, west London, was accused of supplying textbooks describing Jews as “apes” and Christians as “pigs”. The school pledged to remove the offensive pages from the books.

The National Secular Society fears faith schools are using religious education as “another evangelising opportunity”, particularly as loose inspection arrangements mean they can teach the subject the way they like.

Huw Thomas, the head of Emmaus primary in Sheffield, agrees that science at the Catholic and CofE primary is taught in a “spiritual context”, but denies that this amounts to teaching Genesis instead of Darwin.

“We have a spiritual space in the school and we might go there to teach lessons that produce wonders, such as the relative size of the Earth and the galaxy. We might talk about the variety of life and thank God for such a fantastic invention, or we might explain the Big Bang and give thanks, but we are not in a position to impose six-day creationism,” he says.

On the subject of including homosexuality in sexual health and PSHE lessons - a concern raised by the recent select committee report on citizenship - Mr Thomas agrees there is work to be done “but hopes to be in a position to teach the full range of relationships” in future.

Tahir Alam, the education spokesman for the Muslim Council of Great Britain, is less ambiguous: “Parents should have the right to educate their children according to their faith. The state should not seek to alter their views.”

The question of whether the state should impose secular, liberal values on all is at the heart of the faith schools debate. It underlies concerns abut the “fragmenting” effect of minority-faith schools. As one Anglican cleric said: “The fear is if we have more church schools, we have to let the Muslims and Hindus have them too.”

Criticisms of Muslim schools have centred on the belief that they will “ghettoise” children by faith. But currently there are only seven state-funded Muslim schools in the country, compared with 6,791 mainstream Christian schools, and certain sections of the Muslim community are as keen to claim a faith-based education as their Christian and Jewish counterparts. Ultimately, they are a product parents seem to want.

“Certainly it seems to me to be natural justice,” said Revd Jan Ainsworth, the head the Church of England’s education division. “If one religious group is getting state funding, then there’s no reason why the others shouldn’t too.”

* A Muslim teaching assistant lost her appeal against an employment tribunal’s decision that not being allowed to wear a veil in the classroom was not discrimination.

Aishah Azmi, 24, was suspended on full pay after staff at Headfield CofE junior school in Dewsbury, West Yorkshire, said pupils found it harder to understand her. And a High Wycombe 12-year-old has dropped her case against the school that banned her for wearing a niqab.

What the figures add up to

6,841 Number of state-funded faith schools

7 Number of state-funded Muslim schools

400,000 Number of Muslim pupils

10 Estimated number of Muslim pupils who choose to wear the niqab or face veil, according to the Muslim Council of Great Britain

100,000 Number of new school places the Church of England hopes to create over the next 4 years

59 Number of schools creationist group Truth in Science claims are using their materials

Two-thirds Proportion of top-performing primaries that are faith based

5.9 per cent Number of children in top-performing faith schools who claim free school meals. The national average is 11 per cent