Zeid Raad Al Hussein urged Myanmar to end the "cruel military operation" in Rakhine state.
More than 300,000 Rohingya Muslims have fled to Bangladesh since violence erupted there late last month.
The military says it is responding to attacks by Rohingya militants and denies it is targeting civilians.
The violence began on 25 August when the Rohingya militants attacked police posts in northern Rakhine, killing 12 security personnel.
Rohingyas who have fled Myanmar since then say the military responded with a brutal campaign, burning villages and attacking civilians in a bid to drive them out.
The Rohingya, a stateless mostly Muslim minority in Buddhist-majority Rakhine, have long experienced persecution in Myanmar, which says they are illegal immigrants.
Mr Zeid, the United Nations High Commissioner for Human Rights, said the current operation in Rakhine was "clearly disproportionate".
"We have received multiple reports and satellite imagery of security forces and local militia burning Rohingya villages, and consistent accounts of extrajudicial killings, including shooting fleeing civilians," he said.
"I call on the government to end its current cruel military operation, with accountability for all violations that have occurred and to reverse the pattern of severe and widespread discrimination against the Rohingya population," he said.
Latest reports put the number of those who have fled to Bangladesh at 313,000. Aid agencies say they are in desperate need of food, shelter and medical aid, and that current resources are inadequate.