Military sources said the attack targeted the Forward Operation Base in Ngwom village, some 14 km north of the Borno state capital, Maiduguri.
UN refugee agency spokesman Babar Baloch says panicked civilians left the town of Rann over the weekend and crossed into neighbouring Cameroon amid fears of renewed attacks by militants.
Defence ministry says more than 200 militants were killed in air strikes and a further 87 by ground troops since a military offensive began on December 28.
A humanitarian group in Nigeria says it has recorded 10,000 cases of cholera in the country's north.
No group has claimed responsibility for the attack on the village of Mailari in the Guzamala region of Borno. The strike is the latest blow to Nigeria's efforts to defeat insurgencies in the restive country.
Two blasts ripped through the town of Damboa in Borno state on Saturday evening targeting people returning from celebrating the Eid al Fitr holiday, in an attack bearing all the hallmarks of Boko Haram.
It is the first time in years the Nigerian government has said it was talking to Boko Haram about a ceasefire.
Boko Haram kidnapped 110 girls from a school in Dapchi, four weeks ago. Leah Sharibu, 15, was held back on Wednesday when 105 of her classmates were freed by Boko Haram after negotiations.
The Nigerian military has rescued 76 schoolgirls and recovered the bodies of two others, according to three parents, a resident and a local government official.
The disappearance of the schoolgirls, if confirmed, would be one of the largest since Boko Haram abducted more than 270 schoolgirls from the town of Chibok in 2014.
Most of the victims belong to a camp for internally displaced people, who are trying to escape Boko Haram violence. The total number of suspected cholera cases in the country stands at 186, according to the health ministry.
Since the beginning of the year, 83 children have been used to carry out bomb attacks in northeast Nigeria – four times as many attacks as in all of 2016, UNICEF said in a statement.
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