Both the Anglican and Catholic Churches spoke out as the Government issued details of its proposals to set up three new types of schools - community, aided and foundation - as it abolishes opted-out status. The proposals will form part of an Education Bill to be published this autumn.
Ministers expect the bulk of church schools to opt for the new aided status whereby bishops could appoint 11 out of the 21 governors at a secondary school. However, some GM church schools are already considering foundation status - the closest option to the opted-out sector - under which the Church would be able to appoint only three out of 13 governors.
Both the Church of England and the Roman Catholic Church claim the Government is attempting to rewrite the 1944 Education Act, which established the dual system of church and state school operating alongside each other.
Margaret Smart, director of the Catholic Education Service, said: "The Church as a whole believes that these proposals could destroy the dual system as we know it."
Geoffrey Duncan, general secretary of the Church of England board of education, added: "There could be substantial re-writing of the 1944 settlement without such an exercise ever being explicitly stated."
Ministers claim that it would not be sensible for specifically religious safeguards which would apply to all foundation and aided schools to be built into its new framework.
David Blunkett, the Education and Employment Secretary, has also announced more power for parents through new representation on all local authorities and a bigger role on governing bodies.
But the National Confederation of Parent-Teacher Associations wasn't satisfied. Judith Wood, its chair, said: "The parent governor is usually a man; it is not the parent who picks up the children from the playground. We want parents on governing bodies and education committees to be accountable to the rest of parents."