Troops of the Joint Task Force “conducted a cordon and search operation in the Wulari area of Maiduguri about 3:30 am”, Lieutenant Colonel Sagir Musa said.
Thirteen suspected Boko Haram terrorists were arrested and are being investigated.
They also raided another Boko Haram hideout at Popomari district in the same city at dawn, Musa told AFP.
“A suspected Boko Haram terrorist was killed, one AK-47 rifle and some IED (improvised explosive devices) were recovered.”
That raid was carried out about 5:30 am.
Boko Haram has in the past months intensified gun and bomb attacks, especially in northeastern parts of Nigeria where Maiduguri, capital of Borno state, is located.
The group’s deadliest attack yet occurred in the northern city of Kano on January 20, when coordinated bombings and shootings left at least 185 people dead.
An attempt to hold indirect talks between Boko Haram and the government last month appears to have collapsed, with a mediator quitting over leaks to the media and a spokesman for the Islamists saying they could not trust the government.
There has been intense speculation over whether Boko Haram has links to outside extremist groups such as Al-Qaeda’s north African branch.
Nigeria’s population of 160 million is roughly divided between a mainly Muslim north and predominantly Christian south.
In an unrelated operation in the Gomari area of Maiduguri early Tuesday, Joint Task Force troops killed three suspected armed robbers in a shoot-out, recovered one locally-made pistol, a gun and three machetes, Musa also said.