Sarajevo's Scout Film which works with Jolie on the movie said it had submitted the script to the culture ministry of the Muslim-Croat federation after claims it involved a relationship between a rapist and his victim.
"I brought them the script and I am waiting for a positive response as soon as possible, I hope even today," Scout Film's Edin Sarkic said.
War victims were outraged after reports in local media that it described a love story between a Muslim victim and her Serb rapist.
"They no longer have the authorisation to shoot in Bosnia. They will have it if they send us the script with a story which will be different from what we have been told by people who read it," Gavrilo Grahovac, the Culture Minister of the Muslim-Croat federation -- one of the two entities in post-war Bosnia -- told Bosnian radio Wednesday.
Sarkic said that there was no storyline involving the rape of a Muslim girl by a Serb captor, whom she later falls in love with.
"Of course I deny that. It is not in the script," he said.
He added that he spoke to Jolie's production company about the trouble in Bosnia and "they are confident that things will be worked out quickly".
Jolie has already started shooting the film in Hungary and was planning to continue it in Bosnia with scenes in the capital Sarajevo and the central town of Zenica.
The reports about the plot have prompted widespread criticism from victims of wartime rapes.
"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," said Bakira Hasecic, head of the "Women Victims of War" association in Sarajevo.
"We will not allow anyone to falsify our pain," she told Agence France-Presse.
International organisations have estimated that thousands of women were raped during the Bosnian war.
In February 2001, the UN war crimes court for the former Yugoslavia convicted three Bosnian Serbs for crimes against humanity and war crimes after they were found guilty of rape and forced prostitution of Bosnian Muslim women in the southeastern town Foca.
The verdict marked the first time an international court had ruled that rape was a crime against humanity.
The revoking of the film licence has however been criticised in some quarters with actors who rarely get a chance to work with big-name directors attacking what they regard as censorship.
Emir Hadzihafizbegovic, the culture minister for Sarajevo canton who is himself a well-known actor throughout the former Yugoslavia, said he was shocked by the decision.
"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?" he told the Oslobodjenje daily.
Jolie, Hollywood's highest paid actress, will not appear in the as yet untitled love story and has hired mostly local Bosnian actors for the English-language movie.
The 35-year-old, who most recently starred in the spy thriller "Salt", paid a surprise visit to Sarajevo in August when she called on Bosnian leaders to speed up the return of thousands of refugees from the civil war.
