"Congratulations to @manoharparrikar and his team on being sworn in. My best wishes in taking Goa to new heights of progress," Modi tweeted.
Parrikar took oath as the chief minister, forming the government for the fourth time in the state with the support of small parties and Independents.
Congress, which got 17 seats in the 40-member Assembly in the election results declared on March 11, had knocked at the doors of the Supreme Court for stopping the swearing-in but did not get any positive ruling.
Earlier, Governor Mridula Sinha had given 15 days to him to prove the majority in the House.