When I arrive at the South Bank Centre to hear Philip Pullman talk about his new book The Good Man Jesus and the Scoundrel Christ, I half expect to be surrounded by crowds of furious protesters. But rather than being berated for the latest slight he has apparently made to the Christian church, Pullman is enthusiastically greeted by the faithful. There is not even an awkward question - unlike at a recent literary festival in his hometown, Oxford. When asked by an audience member to justify describing Christ as a "scoundrel", the 63-year-old writer insisted "nobody has the right to go through life without being offended".

He has even less time for his detractors when I meet him near Regent's Park two days after his triumphant London appearance.

"Most of the outrage is from people who haven't read it and who refuse to read it on principle so they can continue to be satisfied by their outrage for as long as they can make it last," he says curtly. "But there's been plenty of coverage, which is the main thing. It's varied in approval. Some people like it and some people don't, which is to be expected."

Ironically, the genesis of the story arose from a discussion about Pullman's His Dark Materials trilogy at the National Theatre with the Archbishop of Canterbury, Rowan Williams, who asked whether he would consider exploring the life of the Son of God.

"That was the starting point for me, wondering whether I could do a book about Jesus," recalls Pullman, who had also been approached by Canongate Books to contribute to their Myth series.

The Scottish publisher has previously commissioned novellas by authors like Jeanette Winterson, Margaret Atwood and Alexander McCall Smith, which reinvent the timeless tales of the Greek, Norse and other ancient deities.

"I said I would like to do one but I couldn't think of what to do," says Pullman. "I was thinking of these two things without connecting them until I realised this was the obvious way to do them both together."

But unlike the fantastical adventures of classic heroes and demi-gods like Odysseus and Heracles, the stories of the Bible are not known as the stuff of legend.

"People who believe in them naturally think they are true," says Pullman. "Myths seem to suggest that something isn't true but that isn't really what the word 'myth' means. It actually has a different significance. It's a story that gives an explanation for things, a story that can be told many times in different ways."

Pullman's central conceit is that Jesus had a twin brother, Christ, who lived in his sibling's considerable shadow. Christ secretly documents and engineers Jesus' rise and fall, taking the place of Judas in the narrative as he eventually betrays him to the Romans.

"Christians need to ask themselves if it was necessary for Jesus to be crucified and if they say it was necessary, is that because without that sacrifice, we would not be saved?" says Pullman. "I'd like Christians to imagine being in Jerusalem themselves during the last days of Jesus' life and having the power to magically transport him somewhere so that he would be saved from the fate hanging over him. Would they do that? If they say they wouldn't save him, that they would let him die, are they then as complicit in his death as Judas was? I would save him from death."

While he endowed his main protagonists with mystical abilities in His Dark Materials, Pullman rationalises Jesus' miracles.

"I wanted to write about Jesus as a human figure, a man in a particular situation. A very gifted, charismatic man but an everyman, not a god."

He provides simple explanations for seemingly extraordinary events such as the Feeding of the 5000. Rather than magically transforming five loaves of bread and two fish into enough food for an entire multitude, he merely instructs them to share around what they already have.

"It's not possible to walk on water or to turn water into wine," he says. "That's a fairy tale, it's not a serious piece of historical reportage. It's necessary for the story and for the process of making Jesus appear divine. I have no doubt he had a very strong physical presence, because we've all met people who are like that. Just being in the room with them fills you with energy and makes you feel good. It's not surprising that people who were ill would have felt a lot better around him."

He even claims that the Resurrection was a case of mistaken identity.

"That's the story most Christians would like to believe but I think it just happened by chance. He was in the wrong place at the wrong time. His body disappeared after the burial but there are many ways that could have happened. Perhaps somebody thought they saw him when they went to the cemetery the following morning but they saw someone else who looked like Jesus."

With over 20 books for younger readers to his name, The Good Man Jesus and the Scoundrel Christ represents Pullman's first venture into adult territory.

"I enjoyed writing it because it is a change of direction. I don't know who the audience will be as I don't like speculating about audiences but I guess it will mostly be grown-ups. I also hope there will also be a number of Christians as well as a number of atheists, humanists, Muslims, Jews, Buddhists and even some Scientologists."

Pullman is working on a screenplay of his uncompleted pirate comic strip The Adventures of John Blake, originally serialised in the now-cancelled children's title The DFC. After that, he will be on familiar ground as next up is the long-awaited His Dark Materials sequel, The Book of Dust.

"It's on my desk. After the film script, I will set out to finish it, because I know people have been waiting a long time for it."