"Muslim civilians are now extremely vulnerable," said Navi Pillay.
Her statement came as a Muslim and Christian leader met British Prime Minister David Cameron to lobby for more international assistance.
About a million people - 20% of the population - have fled their homes during months of religious violence.
"I call as a matter of utmost urgency upon the international community to strengthen peacekeeping efforts... Many lives are at stake," said Ms Pillay.
France, the former colonial power, has 1,600 troops in CAR, working with some 4,000 from African countries.
Last week, new President Catherine Samba-Panza said this was not enough.
Since the country's first Muslim leader Michel Djotodia resigned earlier this month, there have been widespread reports of revenge attacks on Muslim civilians.
Members of the Christian majority said they were attacked by members of Mr Djotodia's former rebel group who installed him as leader last year.
But Archbishop of Bangui Dieudonne Nzapalainga and Imam Oumar Kobine Layama, president of the Islamic Central African community, said the unrest was caused by politicians.
"This is not a religious crisis; it's a military-political crisis," Mr Layama told the BBC's Focus on Africa programme.
"We need help for the population, because all our infrastructure is gone, shattered. There is no education, no health care, no medicine," he said before meeting the British prime minister.
"Homes have been razed and famine is on the horizon if we do nothing."
Catherine Samba-Panza was sworn in last week by the interim parliament.
The businesswomen is seen a politically neutral.
CAR is rich in gold and diamonds but years of unrest and poor governance have left most of its 4.6 million people in poverty.
The security situation in the Central African Republic is getting even worse despite the inauguration of a new leader, the UN human rights chief says.