The World War II drama centres on an assassination attempt on Adolf Hitler led by Claus von Stauffenberg (played in the film by Cruise). Valkyrie ran into several stumbling blocks when it started filming last year in Germany.
Defence Minister Franz-Josef Jung wanted to ban the film from lensing in the country as he objected to Cruise's membership with the Church of Scientology. The German government notoriously takes a harsh view on the religion, believing it to be a money-making cult.
Speaking in the latest issue of Empire, Singer admitted: "I don't know how much of what was reported was actually true.
"It was reported that their initial reluctance was something to do with Scientology, but I don't even know to this day if that's really what the problem was."
The film was also met with resistance by some of Stauffenberg's relatives, with son Berthold quoted as saying: "He [Cruise] should keep his hands off my father."
Singer admitted to being disappointed with the comments but said his film received backing from other Stauffenberg family members.
"In reality, we spent a lot of time with the family. There's members of the family in the movie, and we spent intimate time with close members of the family who were there and who had perspective. So, you know, some are supportive and some aren't."
Valkyrie is scheduled for release on October 3.