Many militants were killed in "a fierce encounter" that cost the life of one soldier and wounded five, Col Sani Usman said in a statement.
The military has reported saving about 700 children and women in recent days as soldiers supported by air raids have advanced further into the last hideouts of Nigeria's home-grown Islamic extremists.
It is unclear if those rescued include the schoolgirls kidnapped a year ago from a boarding school in Chibok town. Dozens escaped but 219 remain missing.
"Our troops are unrelenting in their determined efforts of vanquishing Boko Haram terrorists wherever they are," Usman said.
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On Saturday, the first group of 275 rescued about 60 women and the rest children arrived under military escort to the safety of a refugee camp in the eastern city of Yola.
They brought news that some women have died in the rescue missions: Boko Haram militants stoned about 10 women to death for refusing to flee with them, several were accidentally crushed by an armored personnel carrier, and three died when they triggered a land mine.
Most do not know if their husbands and children still are alive or were killed in the attacks when Boko Haram captured them.
They say the insurgents are running out of ammunition, fuel and food as can be seen by the sad state of some critically malnourished children.
One 3-year-old died in a Yola hospital just days after being freed, the BBC reported.