"The suspected sect members came armed and fired sporadic shots that killed over twenty innocent civilians," Haruna Mohammed Sani, spokesman for the Multinational Joint Task Force (MNJTF) said in a statement.
The violence took place on Saturday in Dawashe village, the army lieutenant said in a statement.
He said men from the Civilian Joint Task Force, a vigilante group formed in Boko Haram's bastion Maiduguri to combat the Islamist gunmen who have been terrorising the region for years, entered Dawashe to search for suspects.
Suspected Boko Haram members subsequently opened fire in the village, the spokesman said, adding that the 20 victims were mostly fishermen and traders.
Sani said a dozen other civilians sustained gunshot wounds during the incident but provided no information on casualties among the belligerents.
The toll and circumstances of the incident could not immediately be verified independently.
The MNJTF, a joint military force set up in 1998 to combat border crimes, consists of troops from Nigeria, Chad and Niger.
Its mandate was recently expanded to fight Boko Haram, whose insurgency is estimated to have cost 3600 lives since 2009, including killings by security forces.
