They believe that some local education authorities have already reduced the number of bus passes they give out to denominational pupils - on the pretext that their LEA-devised RE lessons in neighbourhood schools should be good enough for Catholics or Anglicans.
The Government is now known to be investigating five local authorities over a policy which, according to the Catholic Education Service - the official mouthpiece of the Catholic bishops - will have a devastating effect on the Catholic education system. Higher education minister Tim Boswell has also told local authority leaders that he is concerned about cuts to free transport for sixth-formers.
One authority, Brent, admits it will pay for home-school transport only in "exceptional" circumstances.
The CES believes there is now a general threat to the arrangements which have since the Second World War seen pupils get free transport to church schools, often many miles away. The Anglican Church has also expressed concern.
Margaret Smart, director of the CES, said that cuts in transport would strike at the heart of the Catholic secondary schools, many of which were built on green-field sites at the request of local authorities. She said that three London boroughs and at least one county council were considering cutting back on transport.
"They are obviously looking very hard at their budgets, and our concern is that school transport may seem an obvious area to cut. The problem we see is that our schools were built in certain areas - with the agreement of the authorities - on the condition that transport would be provided.
"We have much wider catchment areas and it could seriously threaten the ability of some of our children to travel to Catholic schools, in urban areas as well as rural districts. A substantial number of Catholic families are not particularly well off. It would almost be impossible for the parents to pay. It's going against agreements which have been made earlier, which we would deeply regret.
"We would also seriously resist the notion that because there was one agreed syllabus for religious education that meant that parents' wish to have their child educated in the school of their choice is no longer respected."
Daphne Griffith, a professional officer with the Church of England's Board of Education, said the matter has been raised with the Department for Education which has so far refused to make any public statement.
A policy document from Brent says, "because of the broadly-based and comprehensive nature of Brent's RE syllabus, the LEA takes the view that its schools can provide adequately for pupils of all denominations and are therefore deemed to meet the criteria of 'suitable schools'. It recognises, however, that there may be exceptional cases where the circumstances are such that children will not be able to benefit from education given in a non-denominational setting, and in these cases free transport will be provided. "
A spokeswoman from Brent confirmed that it does not now automatically provide free transport on account of a child's denominational need. The LEA will not pay for a Catholic child to travel past an LEA school with spare places.
Michael Power, deputy director of the CES, said that Brent was breaking the 1993 Education Act, which recognises denominational need. "I'm confident that the DFE will have no choice but to direct Brent to abolish this tendentious policy."