It’s 3pm and the girls at Madani high school in Leicester are trooping out of the gates. They wear white scarves over dark blue djellabas – a shapeless coat worn over trousers. No sign of the boys: they don’t leave for another half an hour.

Boys and girls operate on a different timetable, carefully calibrated to keep the sexes segregated. The architecture at Madani high conspires to do the same: there is a girls’ wing and, in mirror image, a boys’ wing – the two separated by an elegant Arabic-style courtyard with a fountain.

Segregation of the sexes is crucial to the traditional Muslim families who send their children to this state-funded school. Once girls reach puberty, their honour has to be jealously protected, and exposure to the opposite sex limited. To shield them from the drugs, sex and violence that mar British playground culture, traditional Muslim parents will often simply pull their daughters out of nonsegregated schools.

“Each year, hundreds of Muslim girls disappear from the state system,” acknowledges Idris Mears, an educationist and fundraiser for the Association of Muslim Schools UK.

“The drugs, sex and rock’n’roll scene is not an option for Muslim girls,” says Humera Khan, co-founder of Al-Nisa, which offers a wide variety of faith-based services to the Muslim community. “So there is a huge pressure to marry them off early or send them home.”

The parliamentary home affairs committee recently collected statistics on the number of children “not in suitable education” in local authorities with large Muslim populations: 385 in Manchester, 294 in Leicester, 250 in Birmingham. According to Mears, most of them are girls.

How, then, are Muslim girls to be properly educated so that they have a chance of becoming self-confident members of British society? Madani high is one of a small number of Muslim state schools that fuse cultural tradition with a full education under the national curriculum.

State Muslim faith schools give traditional parents who cannot afford private schools the confidence to keep their daughters in school. They raise the chances of Muslim girls going on to higher education. And they give boys as well as girls a sense of belonging to this country, its institutions and values. There are not enough of these schools, however. Although central government claims it wants to provide British Muslim children with a culturally acceptable – but socially empowering – form of education, it is not putting its money where its mouth is. Far from “fast-tracking” Muslim state schools, it is dragging its feet: it took Mohammed Mukadam, head of Madani high, five years to obtain state funding.

Mukadam, who has a daughter of his own, told me he believes passionately in education as the best route to get girls “out of the kitchen and into university”. But he also respects the feelings of those parents who don’t want their children to lose their religious identity or cultural legacy. Muslim state schools, he says, are the solution; traditional Muslim parents feel comfortable keeping their daughters at a school where they can learn to be “British and Muslim”.

As part of the state-school sector, Madani and the six other Muslim schools that receive government funding must pass Ofsted inspections. All seven schools do well in league tables; and, crucially, 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.

Mukadam also ran Leicester Islamic academy, one of the oldest independent Muslim schools in Britain. When he started out there, “not one girl went on to higher education”. From Madani high school, “more than 95%” now do so.

Traditional Muslims do not worry only about their daughters. Many are also wary of keeping their sons in state education. Differences can surface in a mixed gym class or an arts lesson in which they are asked to draw a human body. An ICM poll of British Muslims in 2004 showed that nearly half wanted their children to attend Muslim schools. But, as so few maintained Muslim schools exist, the great majority of the 500,000 Muslim school-age children in England and Wales have to attend secular state education.

Their parents also worry about the Islamophobia that, since the September 11 and July 7 bombings, can creep even into primary schools.

“Everywhere they turn,” says Mears, former head of the Association of Muslim Schools, “children find stereotypes of the Muslim.”

Madani is the perfect vehicle for fighting that stereotype. The building is spanking-new (construction finished last year) and dazzlingly high-tech, with interactive white boards and sophisticated IT equipment in most classrooms. A huge gym caters for basketball and badminton. The grounds are free of litter, the walls of graffiti; and when visitors are guided through the school, the children greet them with the traditional “Salaam alei-kum” (Peace be upon you).

Despite the scarves, the djellabas, the beards and the skullcaps, Madani has its feet firmly planted in British culture: a pink bra stuck on a bulletin board highlights a Breast Awareness campaign.

In one room, a group of girls is waiting to begin extra studies in the school’s own madrasah (supplemental religious school). The take-up is not big but Mukadam is not surprised: traditionally, a madrasah is attached to a mosque and it will take some time before the more devout Muslim families regard a layman’s teaching to be the equal of an imam’s.

Currently, the 700 or so madrasahs in Britain are not inspected by Ofsted, and this has raised fears of child abuse and extremist indoctrination – both in the Muslim community and outside it. However, spokesmen for the Muslim community are wary of criticising the imams who run these schools – their spiritual influence remains enormous in the community.

Mukadam says he has found himself acting as ambassador to the local imams, making the case for girls’ education. “I appealed to the imams: ‘Look, divorce is out there, in high numbers. We must educate our daughters so that they can stand on their own two feet always.”

He dismisses claims that Muslim schools are divisive. Madani’s 570 students are taught that “they’re Muslims, they’re British, and there’s no conflict between the two”. When their faith is treated as a force for good rather than a problem, he feels, students develop a strong sense of identity and self-esteem.

“It is not the school that offers proper teaching of Islam which proves a training ground for terrorism, but the one where Islam is misunderstood or misinterpreted,” says Taj Hargey, who runs the Muslim Education Centre of Oxford.

Hargey this year launched a supplementary school – he won’t call it a madrasah because of the negative connotations – where children are taught the syllabus plus religious education.

“We highlight the passages in the Koran that talk about tolerance and pluralism; reinterpret the passages that we believe have been twisted out of their real meaning,” he says.

Faith Schools Betrayed, a report by Cristina Odone, will be published by the Centre for Policy Studies tomorrow, £7.50

Times Recommends

• Postman Pat moved to a high-tech sorting office
• Saatchi’s old favourites - made in China
• New teaching style gives pupils wake-up call