"Although the war ended in 2009, the re-emergence of terrorism is still a threat," Rajapakse told a defence seminar organised by the military in Colombo.
"While taking every possible counter-measure to prevent the recurrence of terrorism in Sri Lanka, the country also faces the significant challenge of effectively countering the LTTE's propaganda machine."
Sri Lanka's military crushed the Liberation Tigers of Tamil Eelam (LTTE) in 2009 after a nearly four-decade-long struggle for a separate Tamil homeland.
UN rights chief Navi Pillay on Saturday accused the nation's rulers of becoming increasingly authoritarian, with activists facing growing military harassment, four years after the end of the conflict.
Pillay accused the military of intimidating priests, journalists and other civilians as punishment for meeting her during a week-long trip to the island to probe allegations of war crimes.
Sri Lanka has resisted international calls for an investigation into allegations that up to 40,000 civilians were killed by security forces in the final months of fighting. Colombo denies killing any civilians.
It is also facing calls to reduce the size of its military following the end of the war, and to demilitarise former conflict zones in the north and east.
There have been no attacks blamed on the Tigers since the fighting ended, but hundreds of Tamil rebel suspects are still believed to be in custody.
Rajapakse, who was key in driving the military to crush the rebels, said Tamil Tiger sympathisers living abroad have been successfully lobbying and influencing international organisations.
He pointed to the UN Human Rights Council, which passed a resolution in March calling for a probe into the alleged war crimes.
"The recent visit of the UN Human Rights Commissioner (Navi Pillay) is another instance of this (Tamil sympathiser) attention."
He said the possibility of "Muslim extremism" among the island's religious minority was also a cause for concern."Sri Lanka had enough divisions in the past that ultimately led to conflict," Rajapakse added. "We must learn the lessons from our past and ensure that history is not repeated."