Research by The Daily Telegraph suggests that more than half of authorities have abolished – or are considering scrapping – vital subsidies to enable pupils to travel to church schools.
A further quarter of authorities are increasing charges to parents.
Catholic and Church of England groups branded the move “discriminatory” and warned it would bar some children from faith schools altogether as families struggle with spiralling costs.
Parents in areas such as Devon, Hampshire, Wiltshire, Somerset, Worcestershire and Nottinghamshire already have to pay, research shows.
Councils including Warwickshire, Essex, Durham, Stoke and Bolton have announced they will follow suit in the next academic year.
Last month, Rochdale council became the latest to announce similar plans, saying it could save £250,000 by scrapping subsidies to faith schools in 2013.
North East Lincolnshire council is axing a dedicated coach service for children attending Catholic school.
Trafford Council in Manchester has announced plans to remove subsidies to religious schools but not grammar schools, despite threats of legal action from the local Catholic Church.
The Diocese of Shrewsbury, which covers the four Catholic secondary schools in Trafford, threatened to call for a judicial review, saying the decision breached Catholic pupils’ human rights.
Alex Scott, the director of schools for the diocese, said some families would be put off sending their children to Catholic schools because of the cost.
“The council has used its discretionary powers to allow an exemption for children attending the nearest grammar school they are eligible to attend, but has not extended this to all denominational schools,” he said.
“We believe this discriminates against the Catholic parents who decide they want to send their children to Catholic schools.
“There are families that live a long way away from the nearest Catholic school who may well decide that they are unable to afford the cost of sending their children there. This is unfair.”
Town halls have traditionally granted an automatic right to free transport to faith schools as well as children's nearest school if it is too far to walk.
Laws passed in 2006 also require the poorest pupils to be given free transport to any one of their three nearest secondary schools within a six-mile radius of their home and free transport to secondary faith schools up to 15 miles away.
But with mounting pressure on council budgets, many authorities are deciding to remove discretionary free transport to all put the very poorest pupils.
The Telegraph surveyed local authorities across England.
Of the local councils that responded, over half said they had, or were considering, scrapping subsidised travel to faith schools in their area while a quarter said they will be increasing charges to parents.
Gloucestershire council said it will withdraw assistance for new primary school pupils attending Catholic schools only from this year. It said it hoped the decision would help them cut down on the £14m it spends each year transporting its 9,500 Catholic and grammar school pupils.
Up until last year, North East Lincolnshire Council provided a dedicated coach service to children who attended Catholic schools, but a spokesman told the Telegraph: “This historic discretionary Catholic school element of the transport policy was removed as it was deemed unfair and inequitable on the grounds that such a service was not available to pupils of any faith attending other schools in the area.”
Families in Devon, Hampshire, Wiltshire, Somerset, Worcestershire and Nottinghamshire are already having to pay, while those in Warwickshire, Essex, Durham, Stoke and Bolton have announced they will introduce charges in the next academic year.
In many areas, this will result in annual charges of £500 for parents.
Trafford Council has decided to stick to its plans to remove subsidies to religious schools but not grammar schools.
Last month, it emerged that Rochdale was to axe subsidies to schools in its area.
Dale Mulgrew, a local councillor, said it would “potentially could create an education
apartheid”.
"In other Greater Manchester authorities there is an exemption for faith pupils, so why cannot Rochdale follow suit? Otherwise, a two tier system is created,” he said.
Terry Sanderson, president of the National Secular Society, defended the move, saying parents who send their children to faith schools should not be entitled to a “privileged extravagance”.
“Presumably the diocese’s legal advice has since told them that, far from breaching the rights of Catholic children, this subsidy breached the rights of everyone else by denying them the same privilege,” he said.
In a letter to schools earlier this year, Michael Gove, Education Secretary, said: “We want all families to be able to choose the right school for their child.
“We are therefore also reviewing home to school transport so that we can better meet the needs of pupils, ensuring transport is properly targeted to those that need it most.”
A Department for Eudcation spokesman said: "There is funding of £85 million for extended rights to school travel, including funding for pupils from low-income families to attend faith schools.
"The Government has also protected the concessionary travel scheme in full and provided £10 million extra funding for community transport in rural areas.
"It is a matter for local authorities as to whether they choose to provide any additional school transport and whether they charge for it."