The singer, who won the Ramon Magsaysay award for bringing "social inclusiveness in culture" in 2016, will be presented with the honour by Congress president Sonia Gandhi on October 31, Indira Gandhi's death anniversary.
"The 30th Indira Gandhi Award for National Integration for the year 2015 and 2016 has been awarded to T M Krishna, for his services in promoting and preserving national integration in the country," Motilal Vora, member secretary of the advisory committee of the Indira Gandhi Award for National Integration of AICC, said in a statement.
He was also part of a movement to help the Tamil- dominated and war-ravaged northern province of Sri Lanka rebuild its classical music traditions.
An outspoken columnist, Krishna, has written and talked on a wide range of socio-political issues, including women's rights, children's needs, issues that make a society civil or un-civil, and the dangers of the mentality of war and narrow nationalism.
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The Indira Gandhi Award for National Integration was instituted in 1985 by the Congress in its centenary year.
The award is conferred on October 31 for promoting national integration, understanding and fellowship among different communities and cultures of India.
The earlier recipients include spiritual leader Swami Ranganathananda, freedom fighter Aruna Asaf Ali, the Bharat Scounts and Guides, bureaucrat P N Haksar, singer M S Subbulakshmi, former prime minister Rajiv Gandhi (posthumously) and former presidents Dr A P J Abdul Kalam and Shankar Dayal Sharma (posthumously).
Others winners include the Kasturba Gandhi National Memorial Trust (Indore, Madhya Pradesh), musician A R Rehman and Ramakrishna Mission Ashram, Narainpur, Chhattisgarh (jointly), poet Gulzar, scientist Dr M S Swaminathan and activist P V Rajagopal, besides filmmaker Shyam Benegal and lyricist Javed Akhtar.