The Censor Board also asked filmmakers to refrain from depending on agents while applying for censorship.
There have been protests in front of Shenoys Theater in Kochi, and the theatre is being guarded by the police.
The Censor Board secured proof of references to ISIS, Aurangzeb, and Alangir in the film.
The controversial Hindi film based on ISIS recruitment from Kerala, is expected to be released this week.
Censor Board chairperson Prasoon Joshi said the revised version of the film should be submitted to the board soon.
The director said that politicians did not make a fuss if they were subjected to ridicule in movies.
Any filmmaker who is not satisfied with the CBFC recommendations has the right to approach the appellate tribunal and the tribunal can clear the film if it finds the concern valid.
A source adds that the film won't face major hurdles when it comes up for censor certification.
He also said that 'the most restrictive regimes in the world' come up with 'the best films.'