In direct conflict with their wishes, ministers plan to allow church governing bodies and heads to interview parents who want their child to go to a church school.
Critics believe this could lead to selection on social grounds.
In draft admissions regulations ministers say schools should not interview parents as any part of the application or admissions process. However, they add: "Church schools may reasonably carry out interviews, but only in order to assess religious and denominational commitment."
Both churches have said such interviews are not needed.
John Hall, general secretary of the Church of England's board of education, said: "In oversubscribed church schools, priority is given to practising Christians. The parish priest or minister fills a confidential form giving details of a family's religious commitment. The vast majority of church schools do not interview and see no need to."
Margaret Smart, director of the Catholic Education Service, said she would be pursuing the matter with the Government. She said it was a great pity that the churches' position had not been accepted, adding: "Only in exceptional circumstances do we see the need for an interview."
Anne West director of the Centre for Educational Research, at the London School of Economics, said: "I suspect the Government has been lobbied hard by particular schools and individual governing bodies to retain their right to pre-admission interviews. Our concern is that what happens in interviews between heads and parents cannot be verified, and the suspicion is that they can be used for social selection."
In the past, some grant-maintained schools have required parents to complete detailed application forms, seeking information about their jobs and the child's hobbies and achievements.
The GM London Oratory, the school the Prime Minister chose for his sons, has selected pupils on the basis of an interview designed to elicit the extent of parents' commitment to the school's ethos.
There are also anecdotal cases of heads asking parents where they went on holiday, or how many cars they have to assess their socio-economic standing.
Gale Waller, spokeswoman for the Local Government Association, said: "We cannot see the benefit of an interview if we have a better, more transparent, admissions system."
Pauline Latham, chairman of the Grant-Maintained Schools Advisory Committee, said she did not believe most church GM schools were operating pre-admission interviews. "But I'm sure there will be the odd one," she said.
A spokeswoman from the Department for Education and Employment said the interview was to help schools which were oversubscribed to determine the religious commitment of applicants. She said the department has not received any formal submissions from schools calling to keep interviews in its consultation, which ends on December 11.