Nigerian president Muhammadu Buhari on Friday strongly condemned an attack by suspected Boko Haram fighters in the country's northeastern town of Rann, in which three aid workers were killed late Thursday.
The IOM said about 55,000 displaced people were living in a camp near the base at the time of the attack.
Rann, a farming and herding community, is located175 kilometres north of Maiduguri, the state capital.
The army further stated that as the clearance operations progressed, the combined troops tracked the insurgents to Bokko, Daushe and Gava villages, where they unleashed another attack on the fleeing insurgents, killing two of them in a cross-fire and recovered one AK 47 rifle, a magazine, a trolley and unspecified quantity of premium motor spirit in Jerry cans.
MSF said about 40,000 people in Rann were relying nearly entirely on its healthcare services.
"We strongly condemn this attack on selfless aid professionals, who were working in the most hard humanitarian conditions", said Marie-Pierre Poirier, UNICEF regional director for west and central Africa.
The attack comes amid a major military operation to rescue hundreds of girls abducted by Boko Haram from a government boarding school in the neighbouring Yobe State on 19 February.
Three aid workers were injured and a female nurse was missing, feared abducted.
"We strongly condemn this attack on selfless aid professionals, who were working in the most hard humanitarian conditions".
She added that others killed were a medical doctor working as a consultant with UNICEF and an aid worker with the International Committee of Red Cross (ICRC) affiliate organisation.
"According to the United Nations source, two of them [aid workers] had been working with the International Organisation for Migration (IOM), and one was a medical doctor with UNICEF", he said.
About 3,000 aid workers, a lot of them Nigerian nationals, work in northeast Nigeria.
The New York-based Sahara Reporters website said three other soldiers were injured in the attack, which happened on the Damboa-Sabon Gari Road in Borno on 26 February.
He lamented that innocent people were made soft targets, including those engaged in humanitarian services.
Commanders at the time called the bombing a mistake and blamed "the fog of war".
Almost four years ago, Boko Haram kidnapped 276 schoolgirls from Chibok, in Borno State.
The kidnapping and continued attacks in the region have raised questions about the extent of the federal government's claims to have virtually defeated Boko Haram.