Mustapha Karimbe, a civilian helping the Nigerian military fight the terrorist group, said the militants invaded Warwara, Mangari and Bura-Shika in Borno state, slaughtering their victims before setting the villages on fire.
"Most of the victims were slaughtered and most of the wounded [had suffered] machete cuts," Mr Karimbe said.
News of the attacks was slow to emerge due to poor communication as a result of the destruction of telecom masts in the area in previous Boko Haram raids, AFP reported on Wednesday.
Musa Suleiman, another vigilante, said 20 people were killed in Warwara.
He said the attackers killed six people in Bura-Shika and another four in Mangari.
The villages are near Buratai, the hometown of Nigeria's highest military chief Tukur Yusuf Buratai.
Residents of the villages fled to Biu, 30 kilometres away.
Buratai and nearby villages have recently been the targets of deadly raids by Boko Haram, which have left scores dead and entire villages looted and burnt down.
Residents believe the attacks are in response to the pressure that the army chief is exerting on Boko Haram in counter-insurgency military operations.
On Thursday, Boko Haram insurgents killed 14 people, decapitating some of them, when they raided Kamuya village, the hometown of the army chief's mother, and burnt it down.
Since 2009, the terrorists have killed thousands in bombings and shootings in their bid to create a state in Nigeria.