In recent weeks, there has been an upsurge in Boko Haram attacks that have cast further doubt on government and military claims that the jihadists are a spent force.
"A new commander has been appointed for Operation Lafiya Dole", army spokesman Brigadier General Sani Usman said in a statement, identifying him as former military logistics chief Major General Rogers Ibe Nicholas.
Ibrahim is expected to resume as Deputy Chief of Policy and Plans at the Army Headquarters.
Also media analysts, who view the transfer in the light of his performance in the theatre command told journalists that, his predecessor, Major General Lucky Irabor has left a big shoe that would take an extra effort by any General posted to carry.
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The Chief of Army Staff, Lt. Gen Tukur Buratai had in August issued a 40-day ultimatum to the Operation Lafiya Dole Theatre Command to capture Shekau, but he failed to do so when the deadline expired.
The military also suffered a major loss of some 15 soldiers including a commander in November when Boko Haram insurgents attacked troops' location in Sassawa village near the Yobe State capital, Damaturu. About 12 soldiers who escorted the academics were reportedly killed.
About 40 people were killed when a suicide bomber detonated his explosives in a mosque in Yola.
Another suicide bombing was witnessed on December 2 when two teenage suicide bombers attacked Biu market killing at least 18 persons and injuring 52 others.