"All the alarm signals, including the increasing ethnic dimension of the crisis, are flashing red," Zeid Ra'ad Al Hussein warned in a statement.
Burundi has been sliding deeper into violence since President Pierre Nkurunziza announced in April his intention to run in elections in July.
The unrest has intensified since his re-election, with political assassinations on both sides, attacks against the police and summary executions.
But Zeid warned Friday that "deeply worrying new trends are emerging in Burundi, including cases of sexual violence by security forces and a sharp increase in enforced disappearances and torture cases," AFP reported.
He called for an urgent investigation into a spike in violence in Bujumbura last month and witness accounts of at least nine mass graves in and around the capital, including one in a military camp allegedly containing more than 100 bodies of people killed on December 11.
"My office is analyzing satellite images in an effort to shed more light on these extremely serious allegations," Zeid said.
The witness testimony suggests that the toll from the December 11 attacks on three military bases was far higher than the official tally of 87 dead.
The UN puts the number at over 130.
Those attacks meanwhile appeared to have triggered "new and extremely disturbing patterns of violations," Zeid said.
At least 439 people have died in the violence since April 2015 and tens of thousands have fled to neighboring countries out of fear of a return to all-out war.
Burundi plunged into civil war on ethnic lines between majority Hutus and minority Tutsis in 1993, at a cost of an estimated 300,000 lives by the end of the conflict in 2006.