Jolie has already started shooting the as-yet untitled drama in Hungary and planned to film scenes in Bosnian cities Sarajevo and Zenica, starring little-known local actress Zana Marjanovic.
But authorities have banned production from moving to the country amid outrage from women's wartime victims' groups, stemming from confusion over the plot.
Trade publication Variety initially reported the film would tell the story of a Serbian man and Bosnian woman who fall in love in the middle of the Bosnian war, but are driven to take different paths.
However, Bosnian press reported the movie would be a love story between a Muslim victim and her rapist, a Serb.
A spokesperson for the Association of Women Victims of War in Sarajevo tells the Associated Foreign Press, "This is misleading history. Among thousands of testimonies by women raped during the war, there is not a single one that tells of a love story between a victim and her rapist. We will not allow anyone to falsify our pain."
International organisations have estimated that thousands of women were raped during the Bosnian war.
Gavrilo Grahovac, the Culture Minister of the Muslim-Croat federation - one of the two political entities in post-war Bosnia, told Bosnian radio on Wednesday (13Oct10): "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."
Grahovac added revoking the filming licence was a way to "express our disapproval for the shooting of a movie which does not tell the truth and hurts a large number of victims".