Church leaders this week warned that faith schools could be at risk if parents are forced to pay bus fares for their children.
Most local authorities offer free or subsidised transport for children who attend denominational schools more than three miles from their homes. But church leaders say more and more authorities are considering charging parents in a bid to save money.
They fear that as a result faith schools could end up as the preserve of the well-off or remain largely in cities where transport costs are less than in rural areas.
In September, Northamptonshire county council began charging up to pound;272 a year per child travelling to denominational and single-sex schools.
The impact of the charges will be assessed by the council next year.
Essex will next month decide whether to charge parents pound;300 per year per pupil to travel to denominational schools in a move which could save the cash-strapped authority up to pound;1 million. A means-tested charge of pound;40 per pupil is also being considered.
The Roman Catholic Church says if Essex proceeds with the charges it would set a "very unfortunate precedent" which could act as a catalyst for other authorities.
"We fear a momentum could gather pace across the country; a domino effect which could be catastrophic for Catholic schools," said Father George Stokes, RC director for education for Brentwood diocese.
"Poor children and those in rural areas might not be able to go to Catholic schools if these costs are imposed. Catholic schools may eventually be restricted to cities or those who can afford the charges.
"Schools may have to take more non-Catholic children which will dilute the ethos. This could change the nature of these schools forever."
There are six faith schools in Essex and 1,900 pupils have free transport to these or faith schools in neighbouring authorities. Essex says it regretted proposing the charge but it had to make substantial savings because of a lack of government funding.
Parents and teachers have threatened to take legal action on grounds of religious discrimination and over the consultation process, which they claim was unsatisfactory. Governors at St Benedict's college, Colchester, are considering a complaint to the local government ombudsman for not consulting them properly. The council says it has consulted them.
St Benedict's has 820 pupils and the average distance they travel to school is 14 miles. Alan Whelan, principal, said more than 500 children could be affected by charging and as many as 200 could quit. Four have already changed school.
Canon John Hall, chief education officer for the Church of England, said:
"I am very concerned that poor parents could be prevented from sending their children to denominational schools if authorities cut free bus journeys. This could undermine faith schools."
However, the National Secular Society said free transport to denominational schools was a discriminatory use of council funds. It is preparing to launch test cases.
Keith Porteous Wood, the society's executive director, said: "It is entirely unfair that children have subsidised transport on religious grounds."