st Reverend Vincent Nichols, archbishop of Birmingham, said such schools' citizenship lessons "do not make full sense" and risk damaging the fabric of multi-cultural Britain.
"People's culture is only fully explored when the religious roots of that culture are acknowledged and accepted," he writes in an article ahead of a major Catholic education conference in London this week.
"Multi-cultural studies do not make full sense without an appreciation of the meaning and experience of religious belief."
His comments are in direct response to those made by Les Lawrence, the country's most senior education councillor. Mr Lawrence, chairman of the Local Government Association's children and young people's board, said last month that separating pupils on the basis of religion was "not the best way of developing social cohesion".
The Government's backing for the expansion of faith schools has been well publicised. Since Labour came to power in 1997, nine out of 10 applications to open new faith schools have been accepted and a third of its flagship academies are being sponsored by churches and religious groups.
Archbishop Nichols, who is chairman of the Catholic Education Service, backed the policy shift.
He said secular approaches to combating ignorance and prejudice, which have been thrust into the public consciousness following last July's London bombings, did not work and risked creating a "moral vacuum".
"Secular individualism makes rational ethnic discourse very difficult," he said. "The 'good' is what I choose it to be. 'Tolerance' is the only civic virtue. A society does not hold together easily on that basis. What is needed is moral education based on broad and sound principles."
He added: "The secular mind fails to understand the part played by faith in the whole of life. In failing in this regard, it attempts to strip out that faith, while wishing to have regard for a people's culture and artistic expressions."
Archbishop Nichols said the same was not true of the country's 2,000-plus Catholic primary and secondary schools.
"Catholic education does not encourage its students to approach religious faith at arm's length, as if it is something of which to be only suspicious, for such suspicion quickly corrodes the mutual understanding and esteem that true social cohesion actually requires," he said.
Don Rowe, director of the Citizenship Foundation, a charity promoting the subject, said: "We are clear that there should be no artificial separation between the religious and the secular when it comes to discussion of issues in the public domain.
"Citizenship education is about skilling up young people to engage in matters of concern to the community and when they do this, they will do so on the basis of their own values, beliefs and aspirations, whether these are influenced, or based on, religious or secular ideologies."
Lord Adonis, the schools minister, was among the speakers due to address the National Catholic Education Conference in London yesterday.