Eight suspected Islamists were also arrested in a separate incident, a spokesman of a special military unit, Lieuteant Colonel Sagir Musa, said.
“We killed two top commanders of Boko Haram in a shootout outside the city on their way to Damaturu (capital of neighbouring Yobe state) where they planned to attack some military and civilian targets,” he told AFP.
“We recovered a car, five mobile phones and weapons from the terrorists,” he said.
“Eight Boko Haram terrorists are now in our custody from raids we carried out in some parts of the city,” Musa said.
The suspects were allegedly brought in from other states for planned attacks in the city, the hotbed of the sect’s activities.
Musa said the shootout on Wednesday on the outskirts of the city followed intelligence information that the commanders were planning attacks on military and civilian targets in Yobe state where the sect had previously carried out deadly attacks.
Soldiers on Monday said they shot dead a suspected media spokesman for Boko Haram and another high-ranking member outside Kano, Nigeria’s largest city in the north.
Troops involved in the operation said one of those killed was suspected to have been the Boko Haram spokesman who has used the alias Abul Qaqa.
A second man, believed to be the “field commander” for Kogi and Kaduna states as well as the capital Abuja, was also shot and later died from his wounds.
Meanwhile the U.S. said on Thursday that it decided to designate three leaders of Boko Haram as terrorists because their plans had gone beyond discrediting the Nigerian Government.
Mr Johnnie Carson, the U.S. Assistant Secretary of State for African Affairs, made the clarification at a news conference in Abuja.
“We have not designated the entire organisation; we constantly keep that under review, but we have designated the three top leaders we believe to be out establishing broader terrorist networks.
“They have a broader jihadist agenda that goes beyond simply discrediting the Nigerian government.’’
Carson, who spoke on `Presidential Policy Directive on Sub-Saharan Africa’ at the U.S. Embassy, said the activities of the group also served as a major concern to neighbouring countries.
“The issue of Boko Haram is not only of major concern to Nigeria, but to neighbouring countries.
“Boko Haram, we believe, comprises several different kinds of groups.
“We believe that the Boko Haram movement is trying to do everything in its power to show that the government is ineffective in the defence of its people and in the protection of government institutions.’’
Carson reiterated the U.S. Government’s commitment to maintaining a high degree of security presence in its embassies globally.
“The U.S. government will not relent in its contributions to global development. We are reviewing constantly our security processes; it is high; given the current situation.
“As Secretary Clinton has said and as President Obama has made clear, this kind of incident will not draw us back from engaging with the global community.
“We will intensify our efforts to reach out and continue to do works that we think are important to do,’’ he said.
The U.S. on June 22 labelled the acclaimed leader of Boko Haram, Abubakar Shekau, and two others – Abubakar Adam Kambar and Khalid al-Barnawi – as global terrorists.
A statement by the State Department said the designation under Executive Order 13224, “blocks all of Shekau’s, Kambar’s and al-Barnawi’s property interests subject to U.S. jurisdiction and prohibits U.S. persons from engaging in transactions with or for the benefit of these individuals”.