Hearing the petitions filed by Murugan alias Sriharan, T Suthendraraja alias Santhan and AG Perarivalan
alias Arivu that their death sentence be commuted, the high court ordered an interim stay on the hanging pending disposal of the case.
The court has ordered notice to the union government returnable in eight weeks.
On Aug 11, President Pratibha Patil rejected the mercy petitions of Murugan, Santhan and Perarivalan - all linked to the Liberation Tigers of Tamil Eelam (LTTE) - and sentenced them to death for their involvement in Gandhi's 1991 assassination.
Rajiv Gandhi, who was prime minister 1984-89, was killed by a suicide bomber called Dhanu at an election rally in Sriperumbudur near Chennai May 21.
Fourteen other people also lost their lives in the blast.
The three condemned prisoners, who were due to hang September 9, had on Monday moved the high court to commute their sentence to life imprisonment.
Arguing for Perarivalan, senior counsel Ram Jethmalani said the clemency petition was rejected by the President after 11 years and the delay is prima facie wrong.
He said a notice seeking explanation for the delay should be sent.
Urging speedy disposal of mercy petitions, Jethmalani had said earlier that if there was a delay of two years, then the death sentence would be commuted to life imprisonment. This provision was later changed.