Ibn Saleh Ibrahim is believed responsible for the killing of Nigerian civil war hero Gen. Mamman Shuwa in his home in Maiduguri three weeks ago, the Vanguard newspaper reported Thursday.
Lt. Col. Sagir Musa, a spokesman for the Joint Task Force, said in a statement Ibrahim's death occurred Wednesday during a major offensive by forces from the JTF, an air defense regiment and the Department of State.
Several of Ibrahim's lieutenants also were reported killed.
Musa said Ibrahim was in charge of Boko Haram operations in the northeast and northwest sections of Maiduguri, News24Nigeria reported.
A number of weapons, ammunition and explosives were recovered during the operation.
Earlier Thursday, three Igbo traders were shot and killed in another part of Maiduguri by gunmen believed to members of the sect, the Nigerian Tribune reported.
Late Wednesday, a village in the north-central state of Kaduna was attacked by a group of unknown affiliation. Five villagers, including an expectant woman, were killed, said Musa Gaiya, the district head of the area.
He said the killers burned the bodies before fleeing into the bush.