Archbishop Malcolm McMahon has said that Catholic schools "are different" and "for the Catholic community", despite their being funded by all taxpayers.

In an interview with Peter Wilby in the Guardian, McMahon set out the differences between Church of England schools and Catholic schools.

He said the Church of England "runs schools for the wider community" but that "ours are different. They are for the Catholic community".

The Catholic Church welcomed the proposed abolition of the 50% cap which limited faith school's power to reserve places for children by their religious background, and when challenged on why all taxpayers should have to fund discriminatory schools McMahon said that "parents' rights to educate their children as they wish is fundamental."

He deflected criticism that faith schools fuelled segregation by pointing out that "It's not just the faith school sector which is faced with mono-cultural schools. Many community schools comprise predominantly one ethnicity and faith."

Stephen Evans, the campaigns director of the National Secular Society, said: "It's no surprise that Archbishop McMahon wants the taxpayer to fund Catholic schools, but it is alarming to see the Government kowtowing to clerics by agreeing to their demands for more discriminatory faith schools.

"Theresa May's proposals to facilitate the opening of a new wave of religious schools by allowing such schools to select all of their pupil intake on the basis of faith will be a disaster for social cohesion.

"The Catholic Church's vision for education, which involves segregation in schooling and the teaching of dogma, needs to be replaced with a secular approach, in which children of all backgrounds are educated together, religion and belief is taught objectively, and worship is regarded a private matter and not something to be imposed on pupils whilst at school."

The Archbishop, who is the chair of the Catholic Education Service, was also questioned over Catholic schools' record on sex and relationships education.

Wilby pointed out to him that the schools' current curriculum stresses "chastity" and makes no mention of contraception.

McMahon said that teachers in Catholic schools "present arguments for natural methods" but that there would be an "open debate" if a student asked about contraception.

When asked why the Catholic sex education curriculum made no mention of same-sex relationships McMahon said that Catholic schools "would never condemn" gay people but then asked "why would same-sex parents want to send their children to a Catholic school?"

During the interview he was also asked about discrimination against teachers. He said teachers who remarried would "have to follow their consciences" but that there "is no prying".

In December a popular temporary headteacher was forced out because he had divorced and remarried.

Equality Act exceptions allow faith schools to discriminate in both pupil admissions and the employment of teachers.

In Catholic schools, in common with other voluntary aided schools, preference may be given in connection with the appointment, remuneration or promotion of teachers, to those whose religious beliefs or religious practice is in accordance with the tenets of the school's religion or religious denomination or who give or are willing to give religious education in accordance with the tenets of the faith.

Conduct that is "incompatible with the precepts of the Church, or which fails to uphold its tenets, may be taken into consideration in determining whether the teacher's employment should be terminated."

Mr Evans added, "By any 21st Century standard of equality, the degree of discrimination legally permitted on the grounds of religion and belief against teachers and other school staff is unreasonable and unacceptable."

Last year the Equality and Human Rights Commission criticised the extent to which faith schools can discriminate against teachers. It said there should be a genuine occupational requirement before a school could discriminate against staff on religious grounds.