Twinkle, 42, the elder daughter of Rajesh Khanna and Dimple Kapadia, tweeted, "Sir if you can't respect the living, respect the dead - mediocrity is attacking a man who can't respond @NaseerudinShah."
In an interview, Shah had said that 70's was the time when mediocrity came in Hindi films and also when Rajesh Khanna joined the industry, who according to him was a "poor actor".
Twinkle's friend and filmmaker Karan Johar agreed with the actress-turned-author and criticised Shah, saying his comments were in "exceptionally bad taste".
Rajesh Khanna, who was Bollywood's first superstar, died of cancer in July 2012 at the age of 69. He has starred in films like "Baharon Ke Sapne", "Aradhana", "Haathi Mere Saathi", "Amar Prem" and "Aap Ki Kasam" among others.
He won three Filmfare Best Actor Awards and was nominated for the same fourteen times. He was awarded the Filmfare Lifetime Achievement Award in 2005.