The break-in occurred a week after a new UN report detailed crimes against humanity in the East African country and named security forces among the alleged perpetrators.
"A group of armed men went into our office in the middle of the night, at around 2:30 AM," UN human rights office spokesman Rupert Colville in Geneva told The Associated Press.
"The alarm was raised pretty quickly, and they left. Nobody was harmed. An investigation is under way."
The identities of the gunmen were not known, he said. "We don't know what this is all about."
Burundian police said the incident had not been reported.
The UN commission of inquiry report released last week said crimes against humanity, including killings and sexual violence, are being committed in Burundi amid political unrest. It asked the International Criminal Court to open an investigation as soon as possible.
Alleged perpetrators include top officials in Burundi's National Intelligence Services and police force, military officials and members of the youth league of the ruling party, known as Imbonerakure, said the report, which was based on interviews with more than 500 witnesses.
"We were struck by the scale and the brutality of the violations. We also noted a lack of will on the part of the Burundian authorities to fight against impunity," Fatsah Ouguergouz, president of the commission, said last week.
Burundi's government refused to cooperate with the commission and did not allow its members to enter the country.
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