A Church of England diocese has complained to education secretary Nicky Morgan warning that faith schools are under threat.
Some church leaders are worried about new powers that will enable the government to step in and find an academy sponsor if they are failing.
Colin Hopkins, director of education in the Lichfield diocese, warned that faith schools were being treated by the government as a "relic" of the past. Some faith leaders fear that the concerns raised by extremism in Birmingham schools are behind a wider move against faith schools, even though the so-called 'Trojan Horse' schools were not faith schools.
The Education and Adoption Bill currently going through Parliament will compel the education secretary to force a takeover of schools rated by inspectors as inadequate.
There are currently more than 4,500 Church of England, more than 2,000 Catholic, more than 30 Jewish and more than 11 Muslim state maintained schools, a third of the total. There are also few Hindu, Sikh and other faith schools. The Roman Catholic Church ruled out opening any new Catholic academies because of a cap on faith-based admissions. The faiths own the land and the buildings of these schools.
However, Andrew Copson of the British Humanist Association supported the bill.
He said: "With more and more of our state schools being handed to religious organisations under every government of the last 15 years, it is madness to think that they should be placed in some sort of special category forever and immune from every future government policy to improve standards."
The Department for Education said: "No parent should be content with their child spending a single day in a failing school."
Where the department seeks an academy sponsor for a failing school, this would in most cases be a trust run by the diocese of local faith schools. Only if the diocese could not manage this would the governent seek a non-church sponsor and even then the school's religious character would be protected.