Identified as Jarasu Shira, the terrorist chief was arrested at a motor park at about 8.30am along with 10 other suspected members of the group.
It was gathered that the suspects had escorted him to Damboa to connect a vehicle to Biu enroute to Lagos.
Disguised as a cowboy, Shira and his accomplice were arrested by men of the Civilian Joint Task Force (JTF), who are providing support to the Nigerian military fighting the sect group.
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According to sources, Shira is number one on the new list of wanted men by the Nigeria military.
He is believed to be the leader of the Boko Haram militants in Damboa, Chibok and Askira Uba local government areas of Borno state.
It was learnt that the suspects have been handed over to military authorities in Biu, Borno state.