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.
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.
"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 won't allow me to participate in the festivities in Goa," Mr Asrani said in a statement.
When contacted, the "Aligarh" scriptwriter confirmed he had resigned but said he would not like to elaborate further.
Sanal Kumar Sasidharan, who filed a petition in the Kerala High Court against the ministry and IFFI officials yesterday, confirmed Mr 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.
The decision also upset filmmakers whose movies are part of the Panorama section.
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," Mr 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.
Rather than boycotting the festival, they would protest the decision in the festival itself, Mr Vaidya said.
Several jury members also expressed their displeasure.
Film director Ruchi Narain, a member of the jury, said yesterday that she respected Mr 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.
"These films were selected after 21 days of deliberations. I think there must be a protocol to inform the jury chairman of the decision," she said.
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.
He said he was informed that the ministry was dropping the two films but does not know whether others in the jury received the information.
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.
"Nude" depicts the struggle of a woman secretly working as a nude model in Mumbai.
Get the latest election news, live updates and election schedule for Lok Sabha Elections 2019 on ndtv.com/elections. Like us on Facebook or follow us on Twitter and Instagram for updates from each of the 543 parliamentary seats for the 2019 Indian general elections.