He won the Arakkonam lok sabha constituency during 1999 and 2009 elections from the Dravida Munnetra Kazhagam (DMK) party.

In a sting operation conducted in June 2009, it was exposed that one of his medical colleges collected 20 lakh rupees for MBBS.

Jagathrakshakan was first elected to the Tamil Nadu assembly in 1980 when he contested from Uthiramerur as a candidate of Anna Dravida Munnetra Kazhagam (ADMK) under the leadership of MG Ramachandran.

[5] He did not take charge as a minister and after talks with Karunanidhi, the party chief, he was allocated the portfolio of Commerce and industry on 2 November 2012.

He started a research organisation called Alwarkal aaiyuvumaiyam dedicated to the promotion of Tamil culture and art.

After becoming a minister of information and broadcasting, there were allegations that he was trying to float a TV channel and an English newspaper, both of which were not established.

[15][16] Jagathrakshakan is the founder of Chennai-based Accord Group with interests in Hospitality, Pharmaceuticals, Liquor Manufacturing, and Education.

[19] In a sting operation conducted by Times of India in June 2009, it was exposed that one the medical colleges founded by him collected 20 lakh rupees for MBBS admission in violation of Supreme Court order and State legislation.

[20] In September 2012, several news reports alleged that his family is a part of a company named JR Power Gen Pvt Ltd which was awarded a coal block in Orissa in 2007.

"[23] In March 2019, Sri Lanka's BOI (Board of Investment) made an announcement regarding the $3.85 billion plan to build an oil refinery in Hambantota.

This had led to news agencies calling for an explanation from the DMK on the source of funds, especially given Jagathrakshahan's chequered past.

[28] On 12 Sep 2020, Enforcement Directorate seized properties of Jagathrakshakan worth Rs.89.1 crores, due to violation of Foreign Exchange Management Act regulations, in relation to illegal acquisition, holding and transfer of foreign security in Silver Park International PTE Ltd.[29]