The killings were largely blamed on police, intelligence agents, anti-riot officers and militias linked to the ruling party, according to a report issued by UN rights chief Zeid Ra'ad Al Hussein.
The report "details the tragic and comprehensive deterioration in the human rights of the people of Burundi", Zeid told a session of the Human Rights Council in Geneva.
Aside from violence blamed on the security services, the UN rights office documented over the same period 134 murders committed by armed men, likely those opposed to President Pierre Nkurunziza's government.
Burundi has been plunged into a deep crisis since Nkurunziza announced in April 2015 that he was running for a third term. He was re-elected last July.
The violence has forced more than 270,000 people to flee the country, and raised fears of a wider crisis in Africa's volatile Great Lakes region, with the 1994 genocide in neighbouring Rwanda having been fuelled by similar ethnic tensions.
Over the 12-month reporting period, the rights office further recorded 651 incidents of torture.
They were primarily committed between April and July of 2015 and from December to April of 2016, when the repression of opposition supporters was most intense, the report said.
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