The German defence ministry said Cruise has "publicly professed to being a member of the Scientology cult".
Scientology masquerades as a religion to make money, Germany said, but leaders of the church reject this.
Cruise's producing partner Paula Wagner said the star's own convictions had no relation to the film's content.
"Personal beliefs have absolutely no bearing on the movie's plot or themes," she said.
'Heroic and principled'
Scientology has been monitored in Germany in the belief that its activities are "directed against the free democratic order" in the country.
Its status there as a commercial enterprise has prompted repeated protests from the organisation.
Paula Wagner
[Cruise's] personal beliefs have absolutely no bearing on the movie's plot, themes or content
Paula Wagner, Tom Cruise's co-producer
Cruise will play Colonel Claus von Stauffenberg in Valkyrie, leader of the 1944 plot to assassinate Adolf Hitler using a bomb hidden in a briefcase, scheduled for release next year.
German defence ministry spokesman Harald Kammerbauer said that Germany's military "has a special interest in the serious and authentic portrayal of the events of July 20, 1944 and Stauffenberg's person".
Wagner said Cruise's portrayal in the film would be as a "heroic and principled figure", while "Germany is the only place we can truly do the story justice".
"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," she added.
Stauffenberg's son Berthold told the Sueddeutsche Zeitung newspaper earlier this week that he objected to Cruise taking the role because of his involvement with Scientology.
"He should keep his hands off my father," Mr von Stauffenberg said.
Mr Kammerbauer, meanwhile, said that official requests for filming in the country had yet to be received.
