The Muslim Council of Sri Lanka, an umbrella organization 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, intimidation and threats to Muslims, carried out by some Buddhist extremist elements," the MPs said in a joint letter.
It was sent after police on Monday established a new unit to investigate hate crimes after attacks by Buddhist monks on churches and mosques last year raised concerns about religious freedom.
Nationalist Buddhist groups have accused religious minorities of having undue political and economic influence on the island.
Videos posted on YouTube have shown mobs led by Buddhist monks throwing stones and smashing a Christian prayer center in southern Sri Lanka in January this year and attacking mosques while police looked on.
Senior Buddhist monks have also been caught on video threatening violence against their moderate colleagues who advocate tolerance.
The country is emerging from nearly four decades of ethnic war which according to UN estimates claimed at least 100,000 lives between 1972 and 2009.
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.
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.
BA/BA