The Association of Christian Teachers has condemned the decision to stage the production, which depicts the death of a weak and elderly God, to coincide with the Christmas holidays.
Rupert Kaye, the association's chief executive, said: "Philip Pullman actually sets out to undermine and attack the Christian faith. His blasphemy is shameless. This production is in poor taste, given the timing and the content. Teachers should steer clear."
The Church of England has also questioned the timing of the play. A spokesman said: "Given that Christmas is a major Christian festival, His Dark Materials wouldn't seem an obvious choice.
"The possibility that it may cause offence is something we are sure responsible teachers will bear in mind."
Peter Jennings, spokesman for the Catholic Archbishop of Birmingham, said:
"We wouldn't want to be associated with it at all."
Nicholas Hytner, director of the National Theatre, dismissed the criticism:
"Sure, it's anti-clerical," he said. "But it's full of spiritual yearnings.
It's a hugely ambitious attempt to create a new mythology for a generation not served by organised religion."
Philip Pullman said: "My readers are more intelligent than that. The books aren't about the death of God, but about the coming of love. They're about leaving childhood behind and embracing adulthood."
Other members of the church have reacted more favourably to the production.
Pete Broadbent, Bishop of Willesden, welcomed the opportunity for religious debate. He said: "Pullman is a thoroughly good author. The books put questions about life, death and morality on the agenda. It's much better to be talking about religious questions than ignoring them."
His Dark Materials is the National Theatre's most ambitious production to date, costing an anticipated pound;850,000.
Actors Timothy Dalton and Patricia Hodge will take the lead roles, and a variety of special effects will be used to create the illusion that they are journeying through fantasy worlds.