Security forces entered the humanitarian base at 5am on Friday without authorisation and seared the tented camp for close to three hours, the coordinator lamented in a statement.
The Nigerian Army on Friday admitted carrying out a cordon and search operation at a building housing staffers of the United Nations, UN, in Maiduguri but said it was in response to alert on high-profile Boko Haram members.
United Nations expressed serious concern "that these actions could be detrimental to the delivery of lifesaving aid to the millions of vulnerable people in the northeast of Nigeria".
The statement also noted that the search operation was carried out in 29 houses in the general area including a building hosting United Nations staff.
The statement by the Army comes on the heels of UN Humanitarian Coordinator, Edward Kallon's condemnation of unauthorised raid on its main building by soldiers in possible search of Boko Haram leader, Abubakar Shekau.
He said that the clearance operations effort had yielded significant successes in the past weeks.
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The raid was part of the ongoing cordon and search operations in urban and rural areas in the epicenter of the insurgency crisis in and around Maiduguri, the capital of Borno State. On 10th August 2017, theatre command received information from one of its credible sources that some high value BHT suspects had infiltrated into Pompomari Bye-Pass.
"The operation was successfully conducted as over 30 houses were searched".
The Army said while it was not aware that the building belonged to the United Nations, the search was part of cordon and search operations and 30 other buildings were equally searched.
"On the whole, operation in the general area was successfully concluded but no arrest was made because the suspects were not found", Kingsley said.
According to the statement, the search was necessitated by the fact that the Boko Haram Terrorists changed tactics and resorted to targeting military locations, hence the need to intensify clearance operations in the Maiduguri metropolis.
"Members of the public are cautioned against peddling rumours which may cause disaffection and to remain law abiding", he warned.