An imam, Sheikh Mostafa Elazabawy of the Masjid Manhattan mosque, resigned from the museum's advisory panel last month to protest the film. He said in a separate letter to the museum's director that the film "in its present state would greatly offend our local Muslim believers as well as any foreign Muslim visitor to the museum."
The American-Arab Anti-Discrimination Committee called concerns expressed about the documentary "extremely worrisome."
Ibrahim Hooper, a spokesman for the Council on American-Islamic Relations, said museum officials should not reinforce negative stereotypes of Muslims as terrorists.
"Generations of visitors to this facility will be influenced by the contents of the displays and the presentations," Hooper said. "It's going to be very important how Islam and the American Muslim community are portrayed."