In a long editorial, the Vatican newspaper l'Osservatore Romano, also slammed Philip Pullman, the bestselling author of the book on which the family fantasy movie is based.
It was the Vatican's most stinging broadside against an author and a film since it roundly condemned The Da Vinci Code in 2005 and 2006.
The film, which premiered earlier this month in the United States and stars Nicole Kidman and Daniel Craig, is an adaptation of Pullman's acclaimed novel Northern Lights.
The Vatican newspaper said "honest" viewers would find it "devoid of any particular emotion apart from a great chill."
In the fantasy world created by Pullman's trilogy, His Dark Materials, the Church and its governing body the Magisterium, are linked to cruel experiments on children aimed at discovering the nature of sin and attempts to suppress facts that would undermine the Church's legitimacy and power.
Still, some Catholic groups in the United States have called for a boycott, fearing even a diluted version of the book might draw people to read the bestselling trilogy.
The Vatican newspaper said the film and Pullman's writings showed that "when man tries to eliminate God from his horizon, everything is reduced, made sad, cold and inhumane".
The US-based Catholic League, a conservative group, has urged Christians not to see the movie, saying that its objective was "to bash Christianity and promote atheism" to children.
New Line Cinema, a unit of Time Warner Inc, had hoped the film would pull in between $US30 million and $US40 million. It is doing better overseas but New Line sold the foreign distribution rights to help cover the movie's cost.