She expressed her heartfelt condolences to the bereaved family.
Lok Sabha Speaker Meira Kumar has also condoled the death of Khanna, whom she hailed as a legendary actor.
Condoling his demise, Union Minister for Information and Broadcasting Ambika Soni said Khanna will forever remain the super hero of Indian film industry.
"It is with great sadness that I pay my respects to the memory of Rajesh Khanna. He has been such a living force in the film world and has left such a long and rich legacy of film tradition. Language was no barrier. His films were seen all over the country".
"He was fighting the illness and I am so sorry that we lost him. Forever he will be a super hero of the Indian film world," said Soni.
Plans by her I&B Ministry to hold a retrospective of Rajesh Khanna in the presence of the superstar have failed due to his sudden demise.
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Soni said her ministry was in touch with him for doing a retrospective on Rajesh Khanna, but said the actor could not confirm the dates due to his illness.
"My ministry has been wanting to organise a retrospective and were asking him for dates of August 17 and 18. We were in touch with him but since he was in and out of the hospital, he could not confirm the dates with us," said Soni.
Union New and Renewable Energy Minister Farooq Abdullah has also condoled his death and said he was not only a great actor but also an MP.
"His contribution in this industry can never be forgotten. No one can replace him... The country and the world will remember him forever," said Abdullah, while offering his condolences to the bereaved family.