The apex court had sentenced members of the banned Liberation Tigers of Tamil Elam (LTTE) Murugan, Santhan, Perarivalan and Nalini to death in 1999 for the assassination of the former Prime Minister in Sriperumbudur on May 21, 1991.
A Rasthrapati Bhavan spokesperson said the clemency petitions of all three accused were turned down by the President last week.
The apex court had confirmed the death sentence of Murugan, Santhan and Perarivalan while commuting Nalini's sentence to life imprisonment.
The trio, charged with criminal conspiracy and execution of the suicide attack plot, had filed mercy petition before the President after confirmation of sentence by the apex court.
The Home Ministry had sent its opinion on June 21, 2005 which was called back for review on February 23, 2011 and was re-submitted to the President on March 8 this year.
Earlier, in May, the President had rejected mercy petitions of Devinder Pal Singh Bhullar of Punjab and Mahendra Nath Das of Assam following the recommendations from the Union Home Ministry.
Bhullar was sentenced to death by a trial court on August 25, 2001, for plotting terror attacks on Punjab SSP Sumedh Singh Saini in 1991 and the then Youth Congress president M S Bitta in 1993. Das was found guilty of murdering one Hara Kanta Das.