Viduthalai Chiruthaigal Katchi member Thol Thirumavalavan rushed into the well with a giant placard which read: Abolish capital punishment - save Murugan, Santhan and Perarivalan.
The three have been convicted in the assassination of Rajiv Gandhi and had recently appealed to the President to reconsider the rejection of the mercy petitions.
President Pratibha Patil had earlier this month rejected the clemency petitions of the three whose death sentences were confirmed by the Supreme Court in 2000.
The apex court had sentenced members of the banned Liberation Tigers of Tamil Elam Murugan, Santhan, Perarivalan and Nalini to death in 1999 for the assassination of the former prime minister in Sriperumbudur on May 21, 1991.
VCK was an ally of the Dravida Munnetra Kazhagam in the 2009 Lok Sabha polls.