New figures have revealed Muslim pupils outnumber Christian children in more than 30 church schools.
According to the latest available statistics, one Church of England primary school has a '100 per cent Muslim population'.
It has prompted leading education experts to urge some church schools to become secular institutions because it is 'confusing for children'.
St Thomas in Werneth, Oldham, is reported to have no Christian pupils, according to the local diocese, with a 100 per cent Muslim population - though this figure may be 'out of date' according to one governor.
Bishop Bridgeman Church of England Primary in Bolton has a 90 per cent Muslim population, while at Staincliffe CoE Junior School in West Yorkshire 98 per cent of students are reported to come from a Muslim background.
Professor Alan Smithers, director of the centre for education at the University of Buckingham, told the Sunday Times: 'The Church of England has traditionally provided education in this country but now that risks being an uncomfortable experience for the Muslim pupils that fill many of these schools.'
He added: 'It must also be very confusing for the handful of Christian pupils in some of them.
'It would seem logical these schools become secular institutions.'
According to the St Thomas' website: 'St Thomas is a Church of England school and at present most of the children who attend are of the Muslim faith.
'We begin each day with a school worship when we say prayers to recognize the place God has in our lives.
'All children follow a course of Religious Education and we observe both Christian and Muslim Festivals.'