In a message to the brother of 49-year-old film director, he said that Ghosh was an "acclaimed and highly talented director".
"Rituparno Ghosh shall always be remembered for his innovative films which will continue to inspire film-makers. The untimely demise of this promising and creative genius is a huge loss to the Indian film industry, particularly Bengali cinema," Mukherjee said in his condolence message to Indranil Ghosh.
Winner of 12 national and international awards, Ghosh was seen as pioneer of new wave in Bengali cinema with his thought provoking films.
His other award-winning films include 'Dahan', 'Asukh', 'Chokher Bali', 'Raincoat', 'Bariwali', 'Antarmahal', 'Noukadubi', 'Abohoman', 'Chitrangada' and Amitabh Bachchan starrer 'The Last Lear'.