The Anglican and Catholic churches have emphasised to ministers they oppose any measures to provide a fast track for their schools to become grant-maintained.
The two senior church leaders, the Bishop of Ripon, David Young, chairman of the General Synod's board of education, and Bishop David Konstant, head of the Catholic schools service, were given an outline of the plans by Gillian Shephard, the Education and Employment Secretary.
Privately, the two churches are angry that ministers appear to believe their schools are more likely than others to opt out.
The Department for Education and Employment, in a consultation paper, appears to be working on the basis of its own internal research that shows almost a quarter of the 332 Catholic secondary schools have opted out, compared with 15.5 per cent of the country's 2,909 county secondaries.
However, the same paper suggests Church of England schools have not been as receptive, with only 16.8 per cent of the 184 CoE secondaries opting out.
The DFEE proposals include an option to make all voluntary-aided schools grant-maintained from a certain date. Governing bodies would have the opportunity, within a time limit, of deciding to stay with their local authority.
The other options speed up the process of becoming grant-maintained, either by dispensing with the parental ballot or reducing the time limits at the various stages.
The churches are equally unenthusiastic about the two options that are intended to give their schools greater freedom while remaining part of the local authority. The DFEE is suggesting voluntary-aided schools could get a greater proportion of the local authority's spending on schools. Local authorities could be required to delegate to church schools their share of the 15 per cent held centrally to provide services.
The public response of the churches has been muted, pending consultations with the Synod's board of education and the education boards in the Catholic dioceses. Bishop Konstant issued a statement through the Catholic Media Office saying that the Catholic education authorities want their schools to be treated no differently from any other schools on this issue.