The Catholic League has urged parents to boycott the movie which the watchdog group claims to promote atheism as it tells the story of a girl on a quest to kill a character named "God."
"The three novels are extremely anti-faith in general, anti-Christian and anti-Catholic in particular, and pro-atheism," Kiera McCaffrey, director of communications for the Catholic League, told Cybercast News Service. "In each successive book, the anti-God agenda gets progressively stronger."
"Golden Compass" director Chris Weitz had denied pursuing an "atheist agenda" while making the movie, according to the first installment of a Q&A series on an MTV Movies blog. He had also pledged to discontinue as director if he felt he was "watering down" anti-religious themes in the movie's sequels, which would be based from the second and third books of Phillip Pullman's "His Dark Materials" trilogy.
Last Wednesday, in the second installment of the website's Q&A posting, Weitz said he doesn't find the content in the second and third books to be "anti-Catholic."
"I think that an accurate adaptation of 'The Subtle Knife' and 'The Amber Spyglass' would not be anti-Catholic," said Weitz, referring to the titles of the second and third part of "His Dark Materials." "What would be anti-Catholic would be to go out of one's way to attack people's beliefs."
While the Church is clearly the antagonist of the series, the film only refers to the institution as the Magisterium - which is the teaching arm of the Church that interprets the Word of God.
"The Church is portrayed as a totally corrupt, oppressive institution - all churches are. There is no God. It's just an idea that's been concocted to keep people in chains," said McCaffrey.
Critics say the anti-religious references were intentionally removed to make the pro-atheist series more marketable toward children. They also point out that Pullman is an avowed atheist who has publicly stated that his books are a direct response to the "Chronicles of Narnia" series by Christian author C.S. Lewis.
"It's true that Pullman takes issue with dogma and with the abuse of religion for political power, but the critique about dogma applies far more widely than Catholicism or even religion," said Weitz. "The last time that the Catholic church directly exerted political power on a state level was during the middle ages."
Weitz also attempted to defend Pullman, saying that the charge that Pullman wants to "kill God" in the minds of readers is "wrongheaded."
Pullman had said his "books are about killing God," according to a past interview.
"I think Pullman probably has an issue with a certain view of God - which is to say, as a subject worth killing people over," continued Weitz. "In that regard, the institution that I think most closely resembles the Magisterium is the government of Iran."
"I think it's a shame that people are reacting to a movie they haven't seen by attacking a book they haven't understood," he added.
Still, many critics can't ignore the mounted evidence against Pullman including the fact that the novels are based from a line in John Milton's classic poem on Satan's fall from heaven, "Paradise Lost."
Kurt Bruner, co-author of the book, Shedding Light on His Dark Materials, says Pullman's books are definitely anti-religious.
"In many ways, Philip Pullman has taken Satan's side of the argument and has created a world and a story which is all about Satan overthrowing the authority of God," Bruner told Cybercast News Service.
Weitz is expected to answer further questions on the movie in a third installment of questions this Wednesday.
The movie features Nicole Kidman and James Bond star Daniel Craig and opens in theaters on Dec. 7.