The searched raised concerns amongst members of the worldwide community with the United Nations directing its humanitarian workers operating in Borno State to remain indoors.
The UN has accused the army of invading the building, which is used as its humanitarian base, without authorisation.
Kallon said the United Nations had no information regarding the "reason or motivations" for the search, but was working with the government on the issue.
"I am very pleased to report that our relationship of collaboration and trust is intact", Peter Lundberg, the United Nations deputy humanitarian coordinator for Nigeria, said at a briefing in the northeastern city of Maiduguri.
"The humanitarian crisis in Nigeria's north-east is one of the most severe in the world today", said Kallon.
The United Nations' relationship with Nigeria is intact, a U.N. official said on Saturday, despite a military raid on a compound belonging to the worldwide body in the conflict-ridden northeast. The operation was successfully conducted as over 30 houses were searched.
Nigeria forces raid UN Maiduguri base
The meeting arose following a late night cordon and search on the biggest premises of United Nations agencies in Maiduguri by soldiers as part of what the military later described as "a week long search operations for fleeing Boko Haram terrorists conducted on 30 houses in different areas, one of which included a property occupied by the United Nations around Pompamari".
"It has forced the Boko Haram terrorists to change tactics and resort to employment of suicide bombers to target military locations and the populace".
"This necessitated the need to intensify Cordon and Search in Maiduguri metropolis and environment".
Stunt looking security forces including military have raided the United Nations Head Office along Pompomari Bye- Pass road in Maiduguri Borno state. The clearance operations effort has been yielding several successes.
We can't wait to see how this saga would play out.