Ed Balls began his witch- hunt against faith schools last spring, unleashing informants to trawl the country, knock on doors, note down names and infractions. These schools were selective, divisive and a law unto themselves, the Schools Secretary alleged: and now Sir Philip Hunter, the Chief Schools Adjudicator, is to write a report substantiating these allegations, or not, by September.

Many see this inquisition as the latest twist in Labour's internal politics. With Gordon Brown's succession being discussed openly, the ambitious Mr Balls is wooing the strident secularists who make up the old Labour rump. But there is another constituency that he would be foolish to ignore: Britain's 1.8 million Muslims. Faith schools offer a bridge between their religious community and the wider secular society; and for Muslim girls they are the route from the kitchen sink to university.

Last year the Jameah Islamiyah, a small Muslim independent school near Crowborough, East Sussex, was closed, after allegations that its grounds had been used by al-Qaeda terror suspects. Although the school was shut down for educational, not security, reasons, for many this was proof of what David Bell, then Chief Inspector of Schools, had claimed in 2005: that “Traditional Islamic education” did not “entirely fit pupils for their lives as Muslims in modern Britain”. His words fuelled the image of Muslim faith schools being refuges for bearded fanatics who teach children to hate Britain.

The schools that Mr Bell had been referring to were the 50 or so small independent schools that have trebled in number in the past decade. These home-schools are tiny - some with three or four students, learning in someone's kitchen; they are set up by parents worried about Islamophobia in secular state schools.

The school life of Muslim children is the battlefield in which the culture wars between traditionalist Muslims and Britain's secular culture are waged. Muslim children are taught one set of values at home, and a very different one at school: the one demands segregation of the sexes, the other claims anything goes; Muslims require halal or vegetarian food, the secular school will have pork for school dinners, and so on.

Alienated from what they perceive as a hostile system, young Muslims drop out - a third of working-age Muslims in this country have no qualifications; or turn from the state sector to home schooling or the 700 madrassas that are linked to mosques in Britain. Here they can come across the strangest or the most vicious distortions of their faith - and will be all the more receptive to these influences when they are bereft of positive alternatives.

But there is an alternative - even though it is open only to 3 per cent of Muslim children: the seven state-funded Muslim schools. Here children are educated in the basics of their faith in an environment in which being a Muslim does not risk earning them pariah status. As part of the state sector these schools are regulated closely: they must teach the National Curriculum, be inspected by Ofsted and employ properly trained teachers. They also must contribute to community cohesion (anything from opening their buildings to the local Girl Guides or offering English lessons to immigrant parents) and develop links with other local schools.

The result is a group of students who feel Muslim and British. “Seeing their religion treated with respect,” explains Dr Muhammed Mukadam, head of Madani High, a faith school in Leicester, “gives them a sense of respect for all religions. The self-esteem they gain here makes them feel confident in the wider community. And it is not the confident, but the insecure, who grows aggressive.” Evidence bears this out: all but one of the 77 people convicted under the Terrorism Act of 2000 attended a secular state school (the one was home-schooled).

For Muslim girls especially, faith schools play a crucial role. Once their daughters hit puberty, traditional parents will often try to pull them out of school, fearing they might be corrupted by the drugs, sex and violence that are part of playground life. Some will be home-schooled; but many are forced into marriage or sent to live in Pakistan or Bangladesh.

These families find faith state schools reassuring: they know their daughter will be educated, but within a context that prizes her religious instruction and modesty as much as they do. As a result, the proportion of girls in Muslim faith schools who go on to higher education is more than twice as high as in secular state schools.

There are not enough Muslim faith schools to ensure that a whole new generation will benefit. The Government may pay lip service to serving the Muslim community, but in reality it is dragging its feet on bringing more schools into the sector. Sir Philip Hunter's report risks placing even more obstacles in the way of those determined to give young Muslims from poor backgrounds their one chance to learn that their allegiance is as much to Britain as to Islam.

In Bad Faith by Cristina Odone is published by the Centre for Policy Studies today

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