Movies
Defence Minister Franz-Josef Jung previously ruled that the actor could not work on Valkyrie in the inner courtyard of his ministry because of his membership of the Church of Scientology.
The government believe it is a cult pretending to be a religion to make money.
The movie is about a plot in 1944 to assassinate Adolph Hilter. Cruise plays Count Claus von Stauffenberg, who almost managed to kill the Nazi leader. Von Stauffenberg was ultimately killed in the courtyard of the foreign ministry.
Production began in the country last week when Cruise was joined briefly by his wife Katie Holmes and daughter Suri. It is unclear whether there will be filming in the courtyard.
Paula Wagner, chief executive of United Artists Entertainment and a producer on the film, said Cruise's beliefs would not influence the movie.
She added: "We believe the film will go a long way toward reminding the world that even within the ranks of the German military, there was real resistance to the Nazi regime."
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