The militant grouping is alleged to have loaded the victims onto trucks and driving them off, witnesses who fled the violence said on Friday.
The kidnappings came four months after Boko Haram, which is fighting to reinstate a medieval Islamic caliphate in religiously mixed Nigeria, abducted more than 200 schoolgirls from the village of Chibok.
Several witnesses who fled after Sunday’s raid on Doron Baga, a sandy fishing village near the shores of Lake Chad, said militants clothed in military and police uniforms had burned several houses and that 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 (110 mile) road trip on the back of a truck to Maiduguri, capital of the north-eastern state of Borno.
“They were shouting ‘Allah Akbar’ (God is greatest), shooting sporadically. There was confusion everywhere. They started parking our men and boys into their vehicles, threatening to shoot whoever disobeyed them. Everybody was scared.”
They said six older men were also killed in Sunday’s raid, while another five people were wounded.
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 what began as a grassroots movement has rapidly lost popular support as it becomes more bloodthirsty.
Its tactic – kidnapping boys and forcing them to fight and abducting girls as sex slaves – is a chilling echo of Ugandan rebel Joseph Kony’s Lord’s Resistance Army, which has operated 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.
“I am appalled to see reports of another large abduction by terrorists in the northeast of Nigeria.” British Minister for Africa James Duddridge said in an emailed statement.
“Officials at the British High Commission in Abuja are urgently looking into the details. The UK stands firmly with Nigeria as it faces the scourge of Boko Haram.”
Britain and the United States have offered help to try to find the missing Chibok girls, but there has been no success yet.
The kidnappers overpowered local vigilantes who had no support because this is no military presence there, the villagers said.
Talatu Abubakar, another villager who fled to Maiduguri, said the invaders had taunted the men for being unable to defend themselves.
“They were shouting ‘Where is your pride? You people used to be warriors. Today you are all just women, not as brave as we thought’,” he said.
He said that from his Hadeija clan alone, some 47 people were missing and feared to have been abducted.
The raid shows how mobile Boko Haram units can be.
After a military offensive in May last year broke their hold on the area around Lake Chad in the far northeast of Borno state, the rebels relocated to the south of the state, near the Cameroon border nearly 300 km (190 miles) away.
Chibok, where the girls were abducted, is in this area. Their re-appearance in the area demonstrates their ability to move across vast swathes of northeastern Nigeria without being intercepted by the military.
Nigerian forces are overstretched against a determined foe. In the past week they have fought gun battles with Boko Haram Islamists in two key towns in the south of Borno – Gwoza, the security sources said, and the garrison town of Damboa, which the militants sacked a month ago.