"There are various groups who try to create differences in order to undermine our Buddhist values," he said.
"We are a nation familiar with co-existence," Rajapaksa said, while addressing a Buddhist gathering in the southern province.
His comments coincided with the interrogation of a hardline Buddhist monk Galagodaatte Gnanasara of the extremist Bodu Bala Sena group.
Gnanasara was grilled yesterday for over five hours over an alleged anti-Muslim inflammatory speech at the southwestern coastal town of Aluthgama.
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"Properties owned by Muslim were subject to arson attacks. There was a campaign to tarnish the good image of the Buddhists. No one will benefit from discriminating against other religions," Rajapaksa said, adding that there are elements who want to see the country burning with communal flames.
The opposition and Muslim groups charged police with inaction to quell the riot.
The government had vehemently rejected accusations that it was backing the BBS in their campaign of Muslim hatred.