Director Bryan Singer and his cast and crew have been given the go-ahead to shoot the movie -- about the botched 1944 plot to assassinate Nazi leader Adolf Hitler -- in Bendlerblock, the original site where the officers behind the conspiracy were executed.
The government had initially banned the production from filming there after previous bad experiences with film crews.
Some German media had also slammed the casting of Cruise in the iconic role of Claus Schenk von Stauffenberg, who is considered a national hero.
"There was a change of sentiment at the ministry of defense," Thorsten Albig, a spokesman for Germany’s finance ministry, told Bild newspaper. "The latest request by the film team was given a positive answer. There was a different feeling about the project. We will take a closer look with director Bryan Singer at the location and, while ensuring that the dignity of the shrine is protected, see what's possible and what's not."