Zakari, 30, was linked to the recent killing of seven people, including women and children, Xinhua quoted police spokesperson Frank Mba as saying in a statement.
The suspect was arrested Saturday following a massive onslaught by security forces against the activities of insurgents in the Balmo forest in Bauchi State in the northeast, Mba added.
According to him, Zakari was arrested while fleeing from intensive counter insurgency operations around the forest.
The suspect was trained at Gombe forest under the leadership of another fleeing insurgent, Abba Taura, said the police spokesperson, noting that the suspect moved to Balmo forest only three months ago.
Boko Haram is based in northeast Nigeria, north Cameroon and Niger. It seeks to establish an Islamic state ruled by sharia. The group has been declared a terrorist organisation by the US and sanctioned by the UN Security Council.