"We have received complaints from the IFFI jury at Goa that the title of the film on the title card is shown by the filmmaker as S### Durga, which has totally different implications and are effectively undermining and attempting to defeat the very basis of the title registration," the board said in a letter declaring that the film would not be screened "until further notice".
The letter pointed out that a certificate was granted to the movie after the producers agreed to change the title from "Sexy Durga to S Durga" and delete vulgar words.
Speaking to NDTV from the film festival venue, director Sanal Kumar Sasidharan said, "The reason being given to stall the screening is ridiculous. I am ashamed to even fight it out."
The film was cleared for screening by the Kerala High Court, which last week rejected the central government's appeal to scrap it.
"It is ordered that the certified version of 'S Durga' will be viewed by the jury and on the basis, the film will be exhibited in the Indian Panorama of the 48th IFFI," the court had said.
The centre told the high court that the film did not have the necessary clearances and its inclusion at this point was likely to upset the arrangements of the film festival.
S Durga is a road movie that follows the horrifying experience of two hitchhikers, a man and a woman, who encounter two men at the dead of the night. It has won an award at the International Film Festival Rotterdam this year.
Mr Sasodharan says some fringe groups are against the film because they mistakenly believe the title refers to Goddess Durga.