Momodu Bama was killed when the insurgents had a confrontation with soldiers on August 4 in his native home of Bama, military spokesman Lieutenant Colonel Sagir Musa said in a statement.
The high ranking militant, who had a bounty of 25 million naira (USD 156,000) on his head, was killed in northeastern Borno state, Boko Haram's traditional stronghold, the statement said.
Bama "was the terrorists' operation officer and second-in-command to Abubakar Shekau", the Boko Haram chief who has been declared a global terrorist by the US, it said.
The military statement said the killing of Bama could not be disclosed earlier because of the need to properly identify him and that took over a week.
On Sunday, suspected members of the terror group killed 44 people worshipping in a mosque near Nigeria's restive city of Maiduguri.
The oil rich African country's President Goodluck Jonathan had declared a state of emergency in three states of Borno, Adamawa and Yobe, four years after the militant group declared war on the Nigerian state.
Nigeria's 150 million people are evenly distributed among Christians and Muslims.
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