"Buddhists and monks have never been extremists", Rajapaksa said while addressing a religious gathering at Nagollagama in the south.
The Sri Lankan leader's comments come while a Buddhist nationalist group, BBS or 'Buddhist Power Force' in recent months has launched a campaign against what they believe to be growing Islamic extremism.
BBS started the protests against the 'Halal' certifying system in the country alleging that Muslims were trying to impose their ritualistic food products and practices in the Buddhist-majority country.
The President also recalled the massacre of Buddhist monks by the LTTE 26 years ago saying, "Such incidents must be commemorated to remind us of the brutality of terrorism. But not to spread anger and take revenge. These were the types of terrorist acts we suffered for over 30 years."
Some 31 monks were hacked to death by the LTTE in the eastern village of Aranthalawa on June 2, 1987 during the course of the three-decade-long Sri Lankan civil war that killed an estimated 100,000 people.