Burundian officials at the highest level should be held accountable for crimes against humanity and a list of suspects has been drawn up, a U.N. Commission of Inquiry said on Monday.
The commission said there are reasonable grounds to believe crimes against humanity had been committed since April 2015 when President Pierre Nkurunziza said he would seek a third term in office.
The opposition said he was acting unconstitutionally. A government crackdown on protests followed and the ensuing upheaval triggered a food crisis and the exodus of over 400,000 refugees.
"The Commission has reasonable grounds to believe that... crimes against humanity are attributable primarily to state officials at the highest level and to senior officers and members of the National Intelligence Service, the police, the army and the Imbonerakure," the report said.
The Imbonerakure, the youth league of the ruling party, received instructions to commit human rights violations from Nkurunziza's office, it said.
Willy Nyamitwe, senior communication officer in the office of the president, told Reuters the report was an attempt at the "demonization" of Burundi's state institutions.
"Those U.N. experts are mercenaries who act on command... to validate what some people want to see or hear," he said.
"It's war propaganda. They want to show to the world that the situation is tragic while it is calm."
The report of the year-long inquiry, created by the U.N. Human Rights Council in September 2016, was based on more than 500 interviews with victims, witnesses and other sources. The government refused to cooperate.
The commission said it had information about hundreds of executions, hundreds of people being tortured and around 40 rapes. But commission member Francoise Hampson said any attempt to give exact figures was spurious.
The report said the principal perpetrators were the defense and security forces, while the National Intelligence Service had carried out extrajudicial executions, arbitrary arrests and detentions, enforced disappearances, acts of torture and cruel, inhuman or degrading treatment and sexual violence.
"The National Intelligence Service reports directly to the President of the Republic and its operations are managed by a senior administrative officer," the report said.
The commissioners declined to give details of suspects but Commission member Francoise Hampson pointed to people closest to Nkurunziza.
"There's a circle around the president and we have the impression that they have control of a parallel system in the Burundian state, and these people have a certain responsibility," she told a news conference in Geneva.
The commission said ethnic insults had been targeted at Tutsis but that it was "not in a position to establish the existence of a political will to destroy that ethnic group 'in whole or in part', as required by the definition of genocide."
Burundi is under the jurisdiction of the International Criminal Court, although the country is withdrawing in October.
After that, any crimes committed in Burundi will not fall under the ICC's jurisdiction.
The commission called on the ICC to start an investigation as soon as possible.