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Canon Slade Church of England school, in Bolton, says it has been forced to adjust its admission requirements because it is so heavily over-subscribed.
However, its demands fall foul of senior Church of England education officials who are said to be concerned that the school is closing its doors to children from the local community by moving away from an open admissions policy.
But the Rev Peter Shepherd, the school's head, said he had been forced to redefine the rules because too many children were meeting existing entry criteria.
The school has been operating a "sliding scale" of church attendance, under which families get points to qualify for attendance, with 45 being the highest until now.
However, the Rev Shepherd believes next year's eligible intake would exceed the 270 places the school has available and has increased the points needed to 48.
He said: "We have had to find ways to be more discriminating, it is as simple as that, because more and more students every year are meeting the demands.
"It is a bit like having to adjust the marks in the 11-plus depending on how academically strong the candidates are. If you have weaker pupils in any given year you bring the pass mark down, and vice versa.
"Our policy is no different from that. We are having to think of ways of keeping our intake at 270 from the 400 or so who apply every year.
"It is becoming increasingly hard to make decisions about which pupils to allow in. The only way we can do it is by taking into account the church-going habits of the applicants."
Under government guidelines church schools will no longer be allowed to interview prospective pupils as part of the admissions process as of 2005.
They will also be forbidden from holding empty places that are not filled by pupils of that faith.
The Rev Shepherd said the school was so popular because parents valued its ethos and strong academic record. More than 80 per cent of pupils gain five or more A* to C grades at GCSE every year, and the overall pass rate is almost 100 per cent.
Canon Slade takes pupils from more than 130 Christian churches - including Roman Catholics - in Bolton and other parts of Lancashire.
"Our pupils do not have to belong to the Church of England. We look for people who want to attend a school with a Christian ethos," the Rev Shepherd added.
He said that it was up to the clergy in individual churches to advise the school on attendance and it was up to ministers and families to decide together how this was monitored.