The proposal, to come into action next year, will require students to provide a letter from a priest or another form of "suitable evidence of adherence to the faith of the school", The Daily Telegraph reports.
Some 12 schools in Flintshire, North Wales will be a part of the move, which has already caused controversy. Local parents and Roman Catholic priests have accused the council of discriminating against individuals without religious faith.
Schools will be left to work out the finer details themselves, including what is acceptable as proof of faith. The decision has come as the local council attempts to cut costs across the region.
Greg Pope, deputy director of the Catholic education Service for England and Wales, has spoken out about the move and claimed that this year's financial settlement "has been difficult" with "tough decisions" being made. However, he added that he hopes councils "will stand by their obligations to support home-to-school transport".
A council statement said: "Like all councils, Flintshire County Council is under considerable pressure to make savings on its public spending.
"As a result, the council has had to look at every aspect of its work, especially where it is not compulsory for us to provide services and to consider how they can be delivered more efficiently and cost effectively."
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