Christian families are such a rarity in some inner-city communities that two Church of England schools now cater exclusively for Muslim pupils, The Times has learnt.

In many church primary schools in English cities, more than half of the pupils are Muslim. In at least a dozen such schools, more than 80 per cent are from Islamic homes.

Five church schools, in Blackburn, Birmingham, Bradford, Oldham and London, have become 99 per cent Muslim and in two – another school in Blackburn and one in Dewsbury – every pupil is Muslim.

The Church has defended its continuing educational role in such areas and is putting £750,000 towards the construction of a new primary school in Blackburn whose intake will be almost 100 per cent Muslim. The Times has been told that some parishes in the town – where eight of the 24 church primary schools have a majority of Muslim pupils – have questioned the justification for the investment.

It is also understood that at least one Church school no longer observes the requirement to have an act of daily collective worship that is “consistently and recognisably Christian”.

A former school governor in Bradford has warned that some Christians in her city have chosen to send their children to secular schools, fearing they would be isolated at their local, Muslim-dominated church school.

In 1998 the General Synod resolved that church schools should “stand at the centre of the Church’s mission to the nation”. Three years later, the Dearing Commission recommended that “all church schools must be distinctively . . . Christian institutions”.

It said the four-part mission of the Church was to proclaim the gospel, to “nourish Christians in their faith”, to “bring others into the faith” and “to nurture and maintain the dignity of human beings through service”.

The first three aims are not achievable in a school where every pupil is Muslim, because “the beliefs and practices of other faiths must be respected” and “church schools . . . should not be agents of proselytism”.

The Rev Jan Ainsworth, the Church’s chief education officer, said that in such schools the Christian mission was “the honourable but gentler route” of service to the community.

“That is at the heart of the Church’s educational endeavour. [Church schools] were founded for the education of the poor, whoever those poor were. Those schools which today are majority Muslim are still carrying out the Church’s mission of providing service to those who need it. They are schools which take faith seriously.”

Some church schools whose pupils are overwhelmingly Muslim have received glowing Ofsted reports and there is widespread evidence of Muslim parents opting for a Christian school in preference to the secular alternative. Some believe that it is Christians who are missing out.

For four years Ruth Weston was a governor at a church school in the Girlington area of Bradford, where 96 per cent of pupils were Muslim, many still learning to speak English. Mrs Weston, a Christian theologian, said she enrolled her daughter at the school because she wanted to support multiculturalism, but “after much soul-searching” withdrew her after three terms.

“When push came to shove, my daughter’s welfare came first. She was not thriving socially or educationally in an environment where she was the only girl of her religion, culture and first language,” she said.

Most of her white neighbours sent their offspring to a secular school 15 minutes’ walk away, across a busy main road, rather than to their local, almost exclusively Muslim, church school. Mrs Weston said that while some may have been motivated by latent racism, it was “a sad irony” that Christian families felt it necessary to turn their backs on a church school.

The Ven Peter Ballard, Archdeacon of Lancaster and director of education for the Blackburn diocese, said that when the proportion of pupils from one particular ethnic minority background reached 70 per cent at any school, white flight tended to follow. He maintained, however, that the ethnic make-up of most church schools in Blackburn was a close reflection of the surrounding community.

The decision to spend money on a new church school, knowing that almost every pupil would be Muslim, had been taken because “we’re here for the long term”.

“Demographics change. There was certainly a Christian population there at one time and, who knows, 20 years from now the Christians might be back. This is not the time for us to pull out.

“The Church of England has always provided schools for the community. We’ve never provided primary schools [solely] for churchgoing children. That’s been the case for 200 years and we’re not going to change now.”

Class of 2009

— 4,470 (25.3 per cent) of all state primary schools in England are Church of England schools

— 220 (5.8 per cent) of all state secondary schools in England are Church of England schools

— 8 out of the 24 Church primary schools in Blackburn have a Muslim majority

Average age of UK resident by ethnic group

White British 39

Black Caribbean 35

Indian 31

Pakistani 22

Bangladeshi 21

UK households with two or more dependent children

Bangladeshi Muslim 58 per cent

Pakistani Muslim 50 per cent

Black African Christian 29 per cent

White British Christian 16 per cent

Sources: Church of England; Blackburn with Darwen Borough Council; Office for National Statistics

www.timesonline.co.uk/tol/life_and_style/education/article5576412.ece