In the event of Prabhakaran getting caught, he would be tried for offences in the island country and then handed over to India for trial over the killing of former Prime Minister Rajiv Gandhi, he said during an interaction with foreign correspondents in Colombo.
Gandhi was killed by a woman Tiger suicide bomber during electioneering in Sriperumbudur near Chennai on May 21, 1991.
Rajapakse also said there was no need to ban the Liberation Tigers of Tamil Eelam (LTTE) as of now though the options are always open.
The LTTE is not banned in Sri Lanka, though India, the US and the EU have proscribed the outfit.
Asked why the government was not keen to allow foreign observers in the rebel-dominated areas, the Sri Lankan President quipped "but India can go there".
He agreed that international pressure on the LTTE, especially the declaration of the Tigers as the most dangerous group by the US Federal Bureau of Investigation, has helped the Sri Lankan government.
"We welcome that statement from FBI," he said.