The militants slaughtered at least 8 people, including a village elder, during the attack, the security source and residents said.
The villages - Kubirivour, Boftari and Kuburmbalah - are near Chibok town, from where the militants captured more than 200 schoolgirls in 2014.
Sources said the militants were still in control of Malam Fatori town, on the Nigeria-Niger border.
On Sunday, Nigerian troops recaptured the town from the jihadists. However, the militants reinforced their ranks and regained control of the town.