"The Government must urgently do everything it can to arrest this violence, curb the incitement and hate speech which is driving it, and protect all religious minorities," Pillay said.
"I am very concerned this violence could spread to Muslim communities in other parts of the country," she said.
"The authorities must immediately bring the perpetrators of such attacks to book and make it clear to the religious leadership on both sides, and to political parties and the general public, that there is no place for inflammatory rhetoric and incitement to violence," she added.
Pillay's statement came as her panel to probe Sri Lanka's alleged violation of human rights is set to commence its work soonest.
More From This Section
At least three people were killed and nearly 100 others injured when communal clashes broke out in a popular Sri Lankan tourist region.
The ethnic violence between Buddhists and minority Muslims began last night during a rally by majority nationalist group Bodu Bala Sena (BBS) in Muslim-dominated areas of Beruwala, Dharga Town and Aluthgama on the Sinhala-dominated south-western coast in protest against a road rage incident.
The Human Rights Council in March 2014 expressed its alarm at the significant surge in attacks against members of religious minority groups in Sri Lanka, including Hindus, Muslims and Christians.