The commander, whose identity remain unknown, was captured on Wednesday during a operation, and is receiving treatment at a military facility, Xinhua reported citing the statement.
The statement added that 60 fighters of the Boko Haram died in a series of attacks they launched to gain access to Konduga area of northeast Borno State.
Army also seized four motorcycles from the terrorists Wednesday when they fought through an ambush at Benishek in the state.
The terrorists again made an attempt to attack Konduga and its environs on Thursday but the government troops frustrated their desperate efforts.
Troops are currently engaging another large number of heavily armed terrorists trying to enter the town, the statement said.