Imagine, for a moment, that Philip Pullman had the same power as the knife-wielding hero of his fantasy trilogy, His Dark Materials, and he managed to cut a magic doorway through to the parallel universe of British education policy. "Here's what I'd do," says the former teacher, with some relish. "I'd take the whole of the national curriculum, the national literacy strategy, all these assessment targets and attainment scores and God knows what else, put them in a heap and set fire to them."

It's an intriguing daydream, and not only because it mirrors some critics' plans for his own books, deemed "fit for the bonfire" by the Catholic Herald for their supposedly corrupting, anti-religious theme. Pullman, dubbed by a right-wing critic as "the most dangerous author in Britain", clearly has his own crusading zeal - but for him the real danger is in the smothering of young minds.

"The government is not treating our children as human beings, they are treating them as little worker bees to be drilled and filed and assessed, and put into a slot," he complains. "It's all so controlled, it's stifling! We've got to have more mystery in the classroom, allow for a child's imagination to catch fire in unexpected ways. We've got to have that sort of freedom."

It's been many years since Pullman left his job as an English teacher in an Oxford middle school and found his own way to free young minds - in a wooden hut at the bottom of his garden. In 25 years of writing from its cobwebbed, cluttered interior, he's produced dozens of books for children of various ages, but it was the award-winning His Dark Materials trilogy which brought him celebrity status.

Described somewhat misleadingly by its author as "Paradise Lost in three volumes, for teenagers", it is in fact a deliberate reversal of Milton's tale of the war in heaven: this time God loses. Lyra and Will, two children from parallel universes, find themselves called upon to help lead this second rebellion against a senile and pathetic deity encased in a bejewelled life-support machine, who must be deposed in battle so that a "republic of heaven" can be created instead.

They are assisted along the way by a bizarre band of characters including an armoured bear, a gay angel, miniature spies riding dragonflies, wheeled creatures called mulefa and, most importantly, intimate shape-shifting animals called daemons which are the outward manifestations of their own souls.

It's ambitious, theologically nuanced stuff which makes Harry Potter look like Noddy, but it has been devoured hungrily by children and adults alike, many of whom have hailed Pullman as a literary genius comparable to Chekhov, Dickens, Tolkien, Blake and Milton.

Earlier this year the third book of the trilogy, The Amber Spyglass, became the first children's book ever to win the Whitbread prize, and there are plans to produce both a stage version and a film of the trilogy, the latter reportedly through New Line Cinema, the company that made The Lord of the Rings. And just to certify success, it's also earned the publicity-generating tag "semi-satanic" and "truly the stuff of nightmares" from concerned rightwingers and religious groups.

Pullman expected as much - while his primary passion is storytelling, his battle is nothing if not ideological. Adam and Eve's mythic rebellion against God by eating the forbidden fruit from the tree of knowledge was for him an unequivocally positive action, a quest for freedom of the mind. "It's part of our ineradicable human desire to know things, and it's led to every advance we've ever had," he argues.

The opposing view, that humans are dogged by that original sin and we must keep ourselves and each other on a tight rein to avoid disaster, has done incalculable damage to the human race, he feels -not least to our idea of childhood. In schools as in churches, we're protecting our children from the wrong things.

"Children don't know how to play any more," he says. "Every minute of the day is regulated, we've got little children laden with hours of homework, they're not allowed outside because it's dangerous, they're not allowed to just go out and mess around. Poor little buggers, they've got no time at all! Get out of their hair, that's what I say! Just leave them alone, let them go, let them fool around, let them get lost, let them run about in the mud!"

His own young heroes are accordingly much more bruised than the cossetted middle-class darlings of Enid Blyton or CS Lewis. Lyra the tomboy runs wild through the streets of Oxford, while Will lives on his wits while trying to care for his mentally ill mother. Their adventures involve not only fantastic creatures but morally difficult choices, and the agonising process of leaving behind their childhood.

"This is how you teach morality," says Pullman who, contrary to the view of his religious critics, has always taken his responsibility as an author seriously. "You can't say, 'Put your maths books away, we're having a morality lesson now.'