"Want to specially wish the Indian contingent at #Rio2016. Every athlete gave his or her best," Modi wrote on Twitter.
The Prime Minister also congratulated Brazil for hosting a "memorable" Games.
"Special gratitude to the host nation, Brazil for hosting people from across the world and organising memorable #OlympicGames," he said.
India finished 67th on the overall medals tally with only two medals -- a silver and a bronze won, respectively, by P.V. Sindhu in badminton and Sakshi Malik in wrestling.
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