Witnesses reported seeing thick black smoke billowing from the building in Nigeria's capital Abuja at around 11am (BST).
It is believed that the blast was so large that it destroyed a wing of the UN office. Dozens are feared dead.
Police confirmed the explosion on Friday but did not comment on the nature of the blast or whether there were any casualties.
"I can confirm there was an explosion at the U.N. building," a police spokesman in Abuja said.
"We have deployed our policemen and anti-bomb squad. We can't establish how many casualties (there are)."
The building is situated in the same neighbourhood as the US Embassy and other diplomatic posts in Nigeria's capital.
Police and the wounded thronged the three-story building as people began to search for victims. Witnesses reported seeing ambulances taking away victims.
Alessandra Vellucci, a spokeswoman for the UN office in Geneva, said the global body's offices in Abuja had been bombed.
"I saw scattered bodies," said Michael Ofilaje, a UNICEF worker at the building. "Many people are dead."
He said it felt like "the blast came from the basement and shook the building."
The building houses about 400 employees of the U.N. in Nigeria, including the majority of its offices. A local U.N. spokesman declined to comment.
Alessandra Vellucci, a spokeswoman for the U.N. office in Geneva, said the global body's offices in Abuja had been bombed.
She told The Associated Press that there was no word yet on casualties.
The building, located in the same neighborhood as the U.S. embassy and other diplomatic posts in Abuja, had a huge hole punched in it.
Local police spokesman Jimoh Moshood confirmed the blast, but said police were still investigating the cause.
Abuja was the scene of a car bomb at police headquarters in June.
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