But the Islamists gave a fresh indication of the scale of the task, with three separate bombings in the country's religiously tense central region and restive northeast that left at least 35 people dead.
The bombings raised fears of a renewed wave of attacks against vulnerable targets in urban centres, as troops from Nigeria, Niger, Chad and Cameroon make gains against the militants in rural areas.
Jonathan's visit to Baga yesterday, where hundreds of people, if not more, are feared to have been killed, came after his main election opponent, Muhammadu Buhari, accused him of a lack of leadership in the crisis.
"I went... To visit communities devastated by the excesses of Boko Haram," he said. "I just went to see things for myself."
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Jonathan and his administration have been widely criticised for failing to stop the violence, which has seen Boko Haram seize territory in the northeast and attack neighbouring countries.
Presidential elections scheduled for February 14 were delayed for six weeks as the military said the ongoing counter-offensive meant that troops could not provide security on polling day.
On Wednesday, the head of the Nigerian Army, Lieutenant General Kenneth Minimah told troops in Baga after its recapture at the weekend: "The war is almost ended.