A study by the Sunday Times found that a number of Church of England schools had over 90 per cent Muslim population.
The Church of England says around 20 of its schools have more Muslim pupils than any other while the Catholic Education Service has 15.
Many schools now include Islamic prayers in services while teacher training days are often scheduled on Muslim festivals to allow pupils time off.
The Church of England says despite the cultural make up of pupils, its schools still have a Christian ethos.
Rev Nigel Genders said: "It goes back to the principle that we are not faith schools serving a Christian population but church schools serving the local community."
Many Christian schools have faced criticism in recent years for prioritising Christian pupils.
Last year Prime Minister Theresa May introduced legislation which relaxed rules on faith based admission policies in an attempt to encourage the Catholic Church to open more schools.