Witnesses said more people were killed Monday in the shooting, most of them bystanders, at a fish market in Maiduguri, the Daily Trust reported.
The shootout came as Boko Haram members attacked the market, shooting and wounding three civilians, and witnesses reported explosions in and near the area.
Lt. Col. Hassan Mohammed, a spokesman for the Joint Task Force, said the JTF in Borno state defused three improvised-explosive devices around the market and a school, The (Lagos) Guardian reported.
"Large numbers of IEDs and other weapons [have] been recovered. The whole market has been cordoned off and we are currently searching the market to track down the fleeing [Boko Haram] members," Mohammed said.
The exchange of gunfire lasted about 30 minutes, and no JTF members were injured or killed, Mohammed said.
The three civilians who were shot were taken to the University of Maiduguri Teaching Hospital, The Guardian said.
Human Rights Watch says Boko Haram, whose name means "Western education is forbidden," has killed more than 935 people since 2009, while the Nigerian newspaper Vanguard has reported the group has killed more than 2,000 people in northern Nigeria.
The group wants Shariah law throughout Nigeria.