Scriptwriter Apurva Asrani said his conscience doesn't allow him to participate in the film festival, being held in Goa from November 20-28.
Filmmaker Gyan Correa also submitted his resignation, said Sanal Kumar Sasidharan, whose Malayalam film "S Durga" was one of the two films missing from the final selection.
The resignations come a day after Sujoy Ghosh quit as chairperson of the Indian Panorama jury over the ministry's decision to drop the two films that were part of the list submitted by the 13-member jury.
When contacted, the "Aligarh" scriptwriter confirmed he had resigned but said he would not like to elaborate further.
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Sasidharan, who filed a petition in the Kerala High Court against the ministry and International Film Festival of India officials yesterday, confirmed Correa's resignation in a Facebook post.
"I come to know that film maker Gyan Correa, who is also a jury member in IFFI resigned! Rays of hopes in the dark times!," he wrote.
Director Nitin Vaidya, whose film "Muramba" has been selected, called the ministry's decision to drop the two movies "arbitrary and deplorable".
"I & B ministry's decision to drop two films namely Nude by Ravi Jadhav and S Durga by Sasidharan from Indian Panorama at IFFI To be held at Goa is arbitrary, unfortunate and deplorable. Govt should immediately reverse this decision," Vaidya said in a Facebook post.
The director said the two movies were selected by an "eminent jury".
"This is a clear case of suppression of freedom of expression and also disrespect to the creativity that is flourishing in regional cinema despite challenges it is facing," he said.
The makers of the film "Kaasav", also in the Panorama, are planning a protest too.
Several jury members also expressed their displeasure.
Film director Ruchi Narain, a member of the jury, said yesterday that she respected Ghosh's decision to resign.
"I was dismayed by the exclusion of two highly recommended films. It was disappointing that they were just taken off. We sat for three weeks and watched 153 films before making the list," Narain told PTI.
Her colleague in the jury, actor-filmmaker Satarupa Sanyal, said the chairman should have been informed about the decision to drop the two films.
Rahul Rawail, also a jury member, however, had a different take and said the ministry has the right to reject a film.
"We were asked to select 20 films and two stand by films. So we picked 20 films and two as stand by. What they have done is, they have dropped two films and taken the two stand by films. So finally, it is 20 films but all have been approved by the jury," Rawail told PTI.
According to sources in the know, the ministry objected because the film that was supposed to be screened at IFFI was "Sexy Durga" and not "S Durga", the version cleared by the censor board.
The sources added that "Nude" could not make the cut as the submission was "technically incomplete".
"S Durga", which was earlier titled "Sexy Durga", is a road movie that follows the horrifying experience of two hitchhikers, a man and a woman, at the hands of two men. It won the Hivos Tiger Award in the International Film Festival Rotterdam 2017.