Dozens of rebels on motorcycles stormed Matangale, Buraltima and Dirmanti in restive Borno state on Tuesday, opening fire on villagers before looting and burning homes, fleeing residents said.
News of the assault was slow to emerge due to poor communication in the region after Boko Haram destroyed telecoms masts in previous attacks.
"They came around 4:00 pm (1500 GMT) on 20 motorcycles, three gunmen on each, and attacked Matangale before proceeding to Buraltima and Dirmanti," said resident Dala Tungushe.
Matangale was worst hit by the attack as the attackers opened fire at an open well outside the village where residents had gathered to fetch drinking water and do their laundry.
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"The Boko Haram gunmen opened fire on the crowd at the well where they killed around 16 people," said Bulama Karuye, another resident.
"In all, we lost 43 people in the attacks. All the three villages were completely burnt."
He added the number of casualties could have been much higher had some of the villagers not been away at a weekly market around 40 kilometres away.
They said the attackers came from nearby Sambisa Forest, a major Boko Haram stronghold from where hundreds of women and children kidnapped by the militants were rescued during recent military operations.
Troops and local hunters from Damboa pursued the fleeing attackers into the bush and a gunfight erupted.
"The soldiers and the hunters brought back a pickup truck and some motorcycles they recovered from the Boko Haram attackers... But we don't know how many of the gunmen they killed," Tungushe said.