Police arrested 11 suspects in the operation in Damaturu, where Baa Kaka and three others were slain, police commissioner Patrick Egbuniwe said.
"We carried out the raid because of the incessant ambushes on patrol teams by Boko Haram gunmen in the area," he said. "Our intelligence was able to identify the hideout in Damaturu, and we swooped on it."
The militant group has been blamed for more than 1 400 deaths since 2010 as part of its insurgency in northern and central Nigeria.
Recent raids by security forces on Boko Haram strongholds have weakened the group and killed key figures in the movement. Last month, Abu Qaga, the group's spokesperson, was reportedly killed by government forces in Maiduguri.
Boko Haram opposes Western education and lifestyle in Africa's most populous nation. The sect wants the Islamisation of all states in northern Nigeria and the release of its more than 1 000 jailed members as conditions for a peace deal.
Authorities said they are winning the battle against terrorism although Boko Haram has continued to target security forces, churches and educational institutions. – Sapa-dpa