Ministers will stress for the first time that all new state church schools should accept pupils who follow other faiths or who have no religious background.
The move comes after growing pressure on Tony Blair from backbench MPs who said plans to increase the number of church schools would lead to greater segregation of pupils, especially in inner-city areas that saw race riots this summer.
Now guidance will be sent out to school organisation committees, the bodies that decide on new school proposals, urging them to turn down applications from faith groups who refuse to open their doors.
Estelle Morris, the Secretary of State for Education, will spell out the new hard line against segregating pupils by religion when she addresses the Church of England General Synod this morning. Opponents of the plan cited the violent demonstrations outside Holy Cross primary school in north Belfast and race riots in areas such as Oldham and Bradford in the summer as reasons to amend the policy.
Ms Morris, in the first public speech about the plans since they were announced in a White Paper in early September, will say she wants all new faith-based schools to "join the family of schools".
The guidance will insist that all new proposals from faith-based schools should demonstrate a commitment to "inclusivity" – either by accepting pupils of other faiths or none or by outlining arrangements for links with schools of other faiths to enable all communities to be taught together. Preferably, the new faith schools should adopt both proposals, the guidance will argue.
The guidance will cover applications for new schools and those operating as independent fee-paying schools.
Ministers will urge all existing faith-based schools to "follow the spirit of the guidance" and amend their admissions procedures if necessary so that they, too, represent the whole of their community.
A senior aide at the Department for Education and Skills said: "Faith schools must be inclusive and we are prepared to make sure that happens."
Ms Morris will welcome the declaration made by the Church of England, which is planning to open 100 new secondary schools, that all its schools will be inclusive.
Faith schools will be reminded that they must obey the law of the land, which makes it illegal to discriminate on racial grounds. Officials believe an all-white school that refused to admit Muslims or a Muslim school that failed to admit white pupils could be liable to prosecution.
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