The two established churches fear that the provisions in the Bill allowing grant-maintained schools to select up to 50 per cent of their intake will create problems in planning places for children who want to attend a Catholic or Church of England secondary.
According to David Young, Bishop of Ripon and chairman of the Church of England Board of Education, decisions taken by individual schools could override the concerns of the diocese. During the Lords debate on the Bill on Monday, he said: "Most dioceses promote secondary schools to provide denominational education. If the schools choose to use 50 per cent of their intake for selective places, those denominational places are lost.
"If the Government wish the Churches to continue to invest in church secondary schools, they must respect the purposes for which those schools were founded, purposes which are determined by diocesan authorities."
Opposition to parts of the Bill is even greater within the Catholic education service because there are 90 Catholic secondary grant-maintained schools, compared with 30 in the Church of England sector.
The service's director, Margaret Smart, believes individual governing bodies find it difficult to take account of the impact of greater selection across the diocese. "Any decision on changing the intake of a school has an impact across the diocese. The individual school does not have that over-view. It is a question of the common good over individual choice," she said.
However, ministers appear unwilling to make concessions to the churches. Lord Henley, the junior education minister overseeing the Bill in the Lords, insisted that requiring schools to obtain diocesan consent for increased selection or expansion would cut across a fundamental principle of the Bill. Church schools would be advised to consult their diocese, he said.
The bishops have considerable influence in the Lords, but the extent of support for their amendment will not be known until the committee stage of the Bill in 10 days' time. The Government intends to re-introduce the clause lost in the Commons that would allow grant-maintained schools to expand by up to 50 per cent without requiring central government approval. The Bill is likely to return to the Commons at the end of March.