Mr Ghosh, who is abroad, confirmed to NDTV that he has sent a letter to the ministry resigning from the 13-member jury for the Indian Panorama section at IFFI.
Missing from the list of films for the Goa fest announced by the ministry last week were Malayalam movie "S Durga" and Marathi film "Nude", reportedly chosen by the jury to open the festival.
The films' directors Sanal Kumar Sasidharan and Ravi Jadhav have said they are shocked to learn that their films were dropped and that they haven't yet been officially informed.
The ministry has not responded to the allegation that it removed the two firms from the list sent to it by the jury.
Sanal Kumar Sasidharan, who has directed "S Durga", alleged that while the jury's recommendations were sent to the ministry two months ago, it deliberately made the list public late.
"They didn't demand any visual cut, just a few audio beeps, and I agreed to it because it didn't mess with my movie and I wanted it to reach audiences...Where is our freedom of expression and democracy?" said Mr Sasidharan, whose film follows the horrifying experience of two hitchhikers, a man and a woman, in the dead of the night and has won several awards at international film festivals.
Ravi Jadhav said he had been told that his film "Nude," about the struggle of a woman secretly working as a nude model in Mumbai, would open the festival on September 20. He said he has written a letter to the ministry seeking to know why his film was rejected. "Give me some reason at least. It was selected as the opening film. It was a big honour. I am really disappointed and shocked to hear that it has been dropped. Nobody informed me about the decision," Mr Jadhav told PTI.
"Pihu" by Vinod Kapry is now listed as the opening film for the festival.