Known for his ground-breaking work with black holes and relativity, Professor Hawking was the author of several popular science books including "A Brief History of Time". He died at the age of 76 at his home in Cambrige, UK.
In his message, the President said that Hawking's work made the world a less mysterious place.
"Sad to hear of the passing of scientist Stephen Hawking. His brilliant mind made our world and our universe a less mysterious place. And his courage and resilience will remain an inspiration for generations," Kovind said in a tweet.
"His grit and tenacity inspired people all over the world. His demise is anguishing. Professor Hawking's pioneering work made our world a better place. May his soul rest in peace."
Science and Technology Vardhan said: "Saddened by the passing away of #StephenHawking, the greatest scientist of the time, known for his work with black hole and relativity. It is a great loss to the world scientific community."
Born on January 8, 1942, in Oxford, Hawking was diagnosed with motor neurone disease in 1963 at the age of 21.
Doctors expected him to live for only two more years. But Hawking had a form of the disease that progressed more slowly than usual. He survived for more than half a century and long enough for his disability to define him.
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