Philip Pullman's controversial novels should form part of pupils' religious education, the Archbishop of Canterbury said in a speech released today.

Dr Rowan Williams said that it is sometimes easier to clarify what religion is about by first confronting those who are hostile to it.

His remarks were made last night in a private Downing Street address to religious leaders and academics hosted by Tony Blair.

He added: "Should teaching about religion include teaching about its critics? There is every reason for seeing this as a good thing. Clarifying objections is one way of clarifying what is being claimed.

"After all, St Thomas Aquinas begins his account of the 'proofs' for God's existence with the startling words: 'It seems as though God does not exist'."

His Dark Materials, Pullman's trilogy, a Whitbread prizewinner and now a stage hit at the National Theatre, has been branded anti-Christian propaganda by critics.

The author tells the story of Lyra Belacqua, a schoolgirl, who goes on various celestial journeys. It is surpassed in popularity for children's novels only by the Harry Potter books.

Pullman became the first children's author to win the Whitbread Book Award in 2002 for The Amber Spyglass, the last part of the trilogy, which collectively was voted the third best book in the BBC's recent Big Read competition.

Pullman is a self-confessed atheist whose trilogy ends with the death of God. His work has infuriated many religious believers and conservative commentators.

The Catholic Herald condemned his work, which reverses Milton's tale of the war in heaven, as "fit for the bonfire".

Rupert Kaye, chief executive of the Association of Christian Teachers, said that Pullman's "blasphemy is shameless".

But Dr Williams said the tales of Lyra and Will, her companion, could help to address the "inadequacies" of some religious education courses.

"To see large school parties in the audience of the Pullman plays at the National Theatre is vastly encouraging," he said.

"I only hope that teachers are equipped to tease out what in Pullman's world is and is not reflective of Christian teaching as Christians understand it."

The Archbishop rejected a recent call for the teaching of atheism in schools by the Institute for Public Policy Research, the Blairite think-tank.

"To speak as though atheism were a belief system alongside varieties of religious belief is simply a category mistake," he said.

Dr Williams recently saw the two plays of Pullman's work and will stage a public discussion with the author next Monday, after a joint television appearance last year.

Benedict Nightingale, Times theatre critic, said of the National Theatre production: "Recall the famous sketch in which the Monty Python boys materialised with bell, book and candle, hissing 'Nobody expects the Spanish Inquisition'? That's the way Pullman travesties Christianity and the Church."

In his speech Dr Williams compares Pullman's novels with Dostoevsky's Inquisitor parable and Camus's The Plague, both of which are severely critical of organised religion.

These novels, along with Iris Murdoch's The Time of the Angels, could play a part in teaching older pupils about faith, he said.

"You will learn from a reading of Rumi or John Donne or a few pages of Suzuki things that you are unlikely to learn in other ways; and this applies equally to reading critics of belief in general or specific doctrines - hence my appeal to Dostoevsky and Camus and Pullman."