The investigating agency questioned the legal standing of Perarivalan's petition for a recall of his conviction.
Perarivalan, who has spent 26 years in jail, requested the Supreme Court to reopen the case after the CBI said in court that it got "no help from Sri Lanka" in investigating the origin of the bomb plan.
AG Perarivalan was sentenced to life in jail for supplying two nine-volt batteries for the belt-bomb that killed the former prime minister in 1991. He was 19 when he was arrested weeks after the assassination. Last year, he went to a court and said the CBI had dropped the part in his confession where he had said he had "absolutely no idea" what the batteries were for.
Perarivalan spent 14 years in solitary confinement after being sentenced to hang. His death sentence was changed to life term by the Supreme Court in 2014.
Perarivalan told the Supreme Court that the person who made the bomb is in Sri Lanka and hadn't been questioned yet by investigators.
A multi-agency probe was set up in 1998 on the recommendation of the Jain Commission which investigated the Rajiv Gandhi assassination conspiracy.