Tamil rebels were fighting for a separate homeland for ethnic minority Tamils, who are Hindu, on the Sinhalese-majority island.
Seventy percent of Sri Lanka's 20 million people are Sinhalese Buddhists, while Muslims are the second-largest religious group, making up just under 10 percent.
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Rajapakse, who is a Buddhist, warned monks in January last year not to incite religious violence.
However, police broke up a protest denouncing religious extremism last year, sparking opposition allegations that the government was tacitly supporting the violence. The Muslim Council of Sri Lanka, an umbrella organisation of Muslim groups, said 16 out of the 18 Muslim parliamentarians had asked the president to intervene and halt the attacks.
"Muslim parliamentarians wish to bring to your excellency's kind attention the continued hate campaign, intimidatio