Air Marshal Adesola Amosu, Nigeria's chief of air staff, suggested enemy fire may not be to blame, telling reporters that the military was "in full control of the airspace" in the region.
But he said they were keeping an open mind: "There are so many possibilities... We are working on it."
The Alpha Jet, with two pilots on board, left its base in Yola, Adamawa state, at about 10:45 am on Friday and had been expected back by midday the same day.
The officer said they had "an idea of where the aircraft could be" but the arid terrain, weather conditions and fighting in the region were hampering the search effort.
Amosu said he was "hopeful" of locating the jet as soon as possible and that the pilots were still alive.
Nigeria's military is under pressure to reverse recent territorial gains by Boko Haram in the northeast that have led to fears of a potential loss of government control.