Germany has long contended the Church of Scientology is not a religion but an exploitative, profit-based business concern.
Daily Variety is reporting this morning that the German Defense Ministry says the United Artists movie cannot be filmed at German military sites.
Studio Chief Executive Paula Wagner says, "Mr. Cruise's personal beliefs have absolutely no bearing on the movie's plot, themes or content."
Cruise has had trouble with Germans before.
In 1996, German politicians called for a boycott of "Mission: Impossible" and other Cruise films because of his Scientology affiliation.
Photos: Celebs Who Are Scientologists
Cruise met with U.S. Ambassador to Germany Dan Coats in 2002 in an attempt to get German officials to soften their views on the Church of Scientology, which has been officially monitored there since 1997.