He was presented with the 'Order of the Rising Sun, Gold and Silver Star' and certificate by Japanese Ambassador to India Takeshi Yagi in the presence of senior officials of the Department of Science and Technology, which Rao has helped shape up over the years.
"I believe the future of India and Japan are connected together. India has to realise Japan as its greatest strength in Asia and Japan has to realise India is its greatest friends. The future of Asia depends on these two countries working together," Rao said after being bestowed with the honour.
"The scientific work Japan is doing is outstanding. I owe a lot to Japan. Its a great honour received from a great country. I am an admirer of Japan from my childhood and have seen the country grow after the second world war", he said.
The highest Civilian Award of Japan is conferred on academicians, politicians and military officers.
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Rao had been bestowed with about 70 honorary doctorates and is the 'Linus Pauling Research Professor' and honorary president of the Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore.
He is also credit for shaping several premier technical institutes in the country such as IIT Kanpur and has authored over 1000 research papers and 36 books.
Secretary of the Department of Science and Technology Shailesh Nayak said the award is not only an honour for Rao but also an honour to the entire scientific community in India.
Rao, he said, continues to inspire thousands of scientific minds in the country and still as the same curiosity, he said.