The UN Staff said the soldiers forced their way into the building.
The UN is urgently seeking answers from the authorities.
Speaking to reporters separately, the Theatre Commander of Operation Lafiya Dole, Major Gen. Ibrahim Attahiru described the United Nations as one of its strongest and worthy allies in the counter insurgency fight against Boko Haram.
The BBC's Martin Patience in Lagos says one possible reason for the search could be the camp's name - Red Roof.
"Yesterday' s (Friday's) incident was a regrettable 24- hour setback on our well- established relationship with the UN, Governor Kashim admitted, saying, however, "We were quick to take steps in rebuilding our partnership with the United Nations; as chairman of the Borno state security council, I immediately convened a security council meeting at the Government House, Peter Lundberg was in attendance and so where the GOC 7 Div of the Nigerian Army, the Commissioner of Police, the Director SS, the Attorney-General and Commissioner for Justice and the Deputy Governor".
It also said it grounded helicopters - which provide humanitarian assistance to far - flung camps - as a precautionary measure. This necessitated the need to intensify cordon and search in Maiduguri metropolis and environment.
The statement reads: "On August 10, this year, Theatre Command received information from one of its credible sources that some high value BHT suspects had infiltrated into Pompomari Bye-Pass".
Enenche added that the house being referred to as United Nations building was an unmarked accommodation without any sign that it was occupied by the world body, adding that the search operation was conducted peacefully at the premises, when the troops were allowed into it, just like other buildings.
" I am very pleased to report that our relationship of collaboration and trust is intact, and at this stage, we are focused on the work ahead to ensure that the millions of vulnerable people in the Northeast are supported with life-saving humanitarian aid".
"On the whole, operation in the general area was successfully concluded, but no arrest was made because the suspects were not found", the statement said.
He warned against peddling of rumours that could cause disaffection among the various ethnic and religious groups of people in the state.
The eight-year Boko Haram insurgency has driven at least two million people from their homes and nearly seven million need humanitarian assistance.