According to FemaleFirst, the Mission: Impossible star feels that the scenes where Holmes is partially nude goes against their Church of Scientology beliefs.
Cruise, 43, has followed the controversial religion for several years, and Holmes, 27, is quickly converting for her fiance.
The film, entitled Thank You For Not Smoking, shows Holmes in a love scene with actor Aaron Eckhart. When the film was shown at the Toronto Film Festival, the nude scenes were still part of the movie, however, later at the Sundance Film Festival, the scenes were mysteriously missing.
Katie Holmes and Tom Cruise are the happy parents of a new baby girl, Suri. The couple plan to marry soon.