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The abduction of the girls, aged 12 to 15, follows the kidnapping of more than 200 other schoolgirls by the militant group last month, whom it has threatened to sell into slavery.
Lazarus Musa, a resident of the village of Warabe, told Reuters that armed men had opened fire during the raid.
"They were many, and all of them carried guns. They came in two vehicles painted in army colour. They started shooting in our village," Musa said by telephone from the village in the hilly Gwoza area, Boko Haram's main base.
A police source, who asked not to be identified, said the girls were taken away on trucks, along with looted livestock and food.
Boko Haram leader Abubakar Shekau threatened in a video released to the media on Monday to sell the girls abducted from a secondary school on April 14 "on the market".
The kidnappings by the Islamists, who say they are fighting for an Islamic state in Nigeria, have shocked a country long inured to the violence around the northeast.
They have also embarrassed the government before a World Economic Forum (WEF) meeting on Africa, the annual gathering of the wealthy and powerful, in Abuja from May 7-9.
Nigerian officials had hoped the event would highlight their country's potential as Africa's hottest investment destination since it became the continent's biggest economy from a GDP recalculation in March, but the forum has been overshadowed by the crisis over the girls, whose whereabouts remain a mystery.
That has thrown the government's failings on national security into the spotlight just when it sought to parade its achievements such as power privatisation and economic stability to top global business people and politicians.
Boko Haram, the main security threat to Africa's leading energy producer, is growing bolder and appears better armed than ever.
"Many people tried to run behind the mountain but when they heard gun shots, they came back," Musa said. "The Boko Haram men were entering houses, ordering people out of their houses."
In a separate attack early on Monday, suspected Boko Haram gunmen shot or hacked to death at least 13 people in a raid on a market town in the northeast, a survivor said.
April's mass kidnapping occurred on the day a bomb blast, also claimed by Boko Haram, killed 75 people on the edge of Abuja, the first attack on the capital in two years. Another bomb in roughly the same place killed 19 people last week.
Nigerian President Goodluck Jonathan welcomed a U.S. offer to send an American team to Nigeria to support the government's efforts to find the girls, the U.S. State Department said on Tuesday.
The United Nations warned Boko Haram that if they carried out their leader's threat to sell the girls, they would forever be liable to prosecution for war crimes, even decades after the event.
"We warn the perpetrators that there is an absolute prohibition against slavery and sexual slavery in international law. These can ... constitute crimes against humanity," U.N. human rights spokesman Rupert Colville said in Geneva.
The military's inability to find the girls in three weeks has led to protests in the northeast, Abuja and Lagos, the commercial capital. More are expected on Tuesday in Abuja, just as delegates will be collecting their badges to allow them entry to the hotel where the WEF will take place.
British Foreign Minister William Hague reiterated an offer of help to Nigeria on Tuesday, after calling the abductions "disgusting and immoral".
Worsening violence so close to the capital has also put the spotlight on security arrangements for the WEF, with a few delegates cancelling, though organisers still expect most to arrive as planned.
Police and military units were deployed outside the Sheraton hotel, where delegates picked up credentials for the forum. A black pick-up truck carrying four men dressed in black with sub-machine guns patrolled, then sped off.