On 12 March 2020, he was made chief of the BJP Tamil Nadu unit. He is the first from the Arunthathiyar community to hold the post.Murugan was supportive of the Citizenship (Amendment) Act, 2019. He is was not very close to the leaders of Tamil Nadu BJP but was close with the National BJP leaders. Murugan attempted to lead the BJP's high voltage Vel Yatra twice in 2020 to build support for Hindutva politics in Tamil Nadu, but was arrested both times. Chief Minister of Puducherry V Narayanasamy said Vel yatra is a move by BJP to foment communal disharmony. He called the 2020–2021 Indian farmers' protest in Delhi as “false propaganda” in December 2020.
He contested the 2021 Tamil Nadu assembly elections from Dharapuram and lost to DMK's N. Kayalvizhi by 1,393 votes.
On 7 July 2021, Murugan was sworn in as the Minister of State in the Ministry of Fisheries, Animal Husbandry and Dairying and Ministry of Information and Broadcasting during the Cabinet reshuffle. Murugan is the first from the Arunthathiyar community to be made a Union minister since Independence. He had 21 criminal cases against him in August 2021, the most of any minister in the Modi's cabinet. Murugan claimed there were “vested interests” behind the 2020–2021 Indian farmers' protest in northern states in October 2021.
He is member of Rajya Sabha representing Madhya Pradesh.