Rajapaksa's comments came a day after the main Muslim-minority party Sri Lanka Muslim Congress (SLMC) expressed dismay over a hate campaign unleashed by an extremist group targeting the Muslim community.
Addressing a Buddhist religious gathering here, the President said that his government wants to promote racial and religious harmony through religious teachings.
SLMC leader Rauff Hakeem's statement yesterday was a reference to a Sinhala-majority extremist group, Sihala Ravaya's attempt to attack a department store owned by Muslims in the Colombo suburb of Maharagama.
Hakeem who is the Minister of Justice, called for action to nip the anti-Muslim campaign in the bud.
Muslims constitute over 7 per cent of the island's 20 million plus population.