Modi said he is saddened by the demise of Raza "whose contribution to art will always be remembered".
Congress President Sonia Gandhi described his death as a huge loss for the world of art and the country.
In her message, Gandhi remembered Raza as an outstanding creator of the golden years for Indian modern art.
94-year-old Raza was suffering from old-age related ailments and was in the ICU of a private hospital here for the last two months.