Asrani's resignation comes a day after filmmaker Sujoy Ghosh said he had quit as chairperson of the Indian Panorama jury.
Asrani said his conscience doesn't allow him to participate in the film festival, being held in Goa from November 20-28.
"I stand with the chairman of the jury. We had a responsibility towards some very sincere films, and somewhere we have failed them. My conscience wont allow me to participate in the festivities in Goa," he said in a statement.
The information and broadcasting ministry has overruled the recommendation of the 13-member jury and pulled out Malayalam movie "S Durga" and Marathi film "Nude" from the 48th edition of the International Film Festival of India.
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The jury submitted its list to the ministry on September 20-21, but the line-up was made public only recently and without the name of the two films, a jury member disclosed.
Yesterday, "S Durga" director Sanal Kumar Sasidharan filed a petition in the Kerala High Court against the ministry and IFFI officials.