The kidnappings come four months after Boko Haram, which is fighting to reinstate a medieval caliphate in religiously mixed Nigeria, abducted more than 200 schoolgirls from the village of Chibok.
Several witnesses who fled after the Sunday's raid on Doron Baga, a sandy fishing village near the shores of Lake Chad, said the militants had burned several houses and that as many as 97 people were unaccounted for.
"They left no men or boys in the place; only young children, girls and women," said Halima Adamu, sobbing softly and looking exhausted after a 180 km road trip on the back of a truck to the northern city of Maiduguri.
"There was confusion everywhere. They started parking our men and boys into their vehicles, threatening to shoot whoever disobeys them. Everybody was scared."
The villagers said six older men were also killed in Sunday's raid.
Boko Haram, seen as the number one security threat to Africa's top economy and oil producer, has dramatically increased attacks on civilians in the past year, and the once-grassroots movement has rapidly lost popular support as it gets more blood thirsty.
Its solution - kidnapping boys and forcing them to fight and abducting girls as sex slaves - is chilling echo of Uganda's Lord's Resistance Army, which has operated in the same way in Uganda, South Sudan and central Africa for decades.
The military did not respond to a request for comment. A security source said they were aware of the incident but were still investigating the details.
SHI/SHI