The Oscar-winning actress - who is making her directorial debut with the untitled project, which tells the tale of a couple who meet each other just as the Bosnian war begins in 1992 - has run in to trouble over claims her movie is to feature a Serbian rapist and his Muslim victim.
The Women Victims of War group has blasted the project claiming it will be guilty of "misleading history".
Gavrilo Grahovac, Culture Minister of the Muslim-Croat federation - who met with representatives from the group - revealed he cancelled the permit because no screenplay had been attached to the application.
He added: "They no longer have the authorisation to shoot in Bosnia.
"They will have it if they send us the scenario with a story which will be different from what we have been told by people who read it."
However, Edin Sarkic, who represents Sarajevo`s Scout Film and is working with the 35-year-old actress on the movie, has denied it contains the specified scene.
He said. "Of course I deny that. It is not in the script."
He added: "I brought them the script and I am waiting for a positive response as soon as possible, I hope even today."
Emir Hadzihafizbegovic, Culture Minister for Sarajevo, is appalled by the decision to revoke Angelina`s permit.
He said: "Is this how we thank Angelina Jolie ... for treating a Bosnian tragedy that has already been forgotten by the world ... for hiring five or six Bosnian actors in her movie?"
Angelina is currently filming the project - for which she wrote the screenplay - in Hungary.