The state-run Star Theatre in Kolkata on Saturday stopped the screening of Bengali film Teen Kanya on the premise that it sends out an anti-state message.
West Bengal education minister Bratya Basu features in the movie.
The movie, released Friday, is a suspense thriller directed by Agnideb Chattopadhyay and stars noted actresses Rituparna Sengupta and Ananya Chatterjee.
Though it continues to be screened in private theatres, it has been pulled out of the Star Theatre.
"I was told by Star Theatre authorities that the film was anti-government, and so it would not be screened there," said Chattopadhyay.
The film is said to bear a resemblance to the real-life Park Street rape case, in which an Anglo Indian woman was raped in a moving car.
Chief minister Mamata Banerjee received criticism from all quarters after she dubbed the incident "fabricated".
The filmmaker said he was dismayed and shocked that the government could take such action.
"I am totally at a loss. I am not a political filmmaker. Moreover, Education Minister Bratya Basu has played an important role in the movie, and would never have agreed to act in it if there were indeed something objectionable or against the government," said Chattopadhyay.
"The movie has been certified by the censor board. They have not deleted a single scene or suggested any cuts. In fact, they appreciated the movie saying it had been filmed from a neutral point of view," Chattopadhyay said.
The Trinamool Congress-run Kolkata Municipal Corporation (KMC) which took over the heritage theatre in April this year, however, has washed its hands of the matter.
"The KMC has nothing to do in this matter. Those entrusted with the administration of the theatre have taken the decision," Mayor Sovon Chatterjee said.
The actresses also condemned the move to pull the movie out of the Star Theatre.
"The character I am playing at one point says: 'I have full faith in the law and order system'. How can a movie with such dialogues be anti-government," said Ananya.
"I never felt that there was a political message in the film. People should have watched the film before taking a decision. The film was extremely well received by the audience and the shows on Saturday had been booked in advance. I am shocked," said Rituparna.
Rebel Trinamool Congress Parliamentarian Kabir Suman also condemned the move and said the incident reflected the 'growing intolerance' of the Banerjee government.