The objective of the search could not be determined but it could damage an already tense relationship between the military, the United Nations and aid groups tackling one of the world's largest humanitarian crises sparked by the Boko Haram conflict.
"Members of the Nigerian security forces entered a United Nations base for humanitarian workers in Maiduguri ... without authorisation," said Samantha Newport, a spokeswoman for the UN Office for the Coordination of Humanitarian Affairs.
The security forces, who arrived at about 5 a.m., "carried out a search of the camp and left at about 0800 hours," she said, adding that the UN has no information on the reason for the unauthorised search.
"The United Nations is extremely concerned that these actions could be detrimental to the delivery of lifesaving aid to the millions of vulnerable people in the northeast of Nigeria," Newport said.
The UN's top representative in Nigeria, the humanitarian coordinator, is communicating with the government about the incident, said Newport.