The government recently stipulated that schools must now teach two, rather than one, religion for the GCSE RE course. Other religions must still be taught in RE lessons.
The Catholic Education Service (CES) has been criticised by Muslim and secular leaders for choosing Judaism instead of Islam, given that the latter is the second largest religion in the UK after Christianity, and that Muslim children can form up to 90 percent of the student body in some Catholic schools in Britain.
Around one in ten schools in the UK are Catholic ones.
Paul Barber, from the CES, told Christian Today: "We are fully supportive of the new, more academically rigorous RE GCSE.
"Teaching Judaism as the second religion will ensure that schools continue to comply with the Catholic Bishops' Conference Religious Education Curriculum Directory.
"This is so our pupils can gain a thorough understanding of the richness and breadth of 2000 years of Catholic theology and culture.
"It is because our pupils have a thorough knowledge and understanding of the Catholic faith, they are able to be more accepting of others with different faiths."
However Sir Iqbal Sacranie, the former secretary general, told The Express: "This is not a good decision.
"It does not reflect well on the messages that are coming out from the Church for greater tolerance of other faiths.
"This is a difficult time for religions and the last thing you would expect is a major faith making such a statement."