Thousands of troops and police officers deployed in the emergency swiftly forced the extremists out of major urban centers, but the campaign, which includes aerial bombardments and ground assaults, has been struggling to flush them out of hideouts in forests and caves.
Amnesty International and an investigation by The Associated Press of mortuary records show hundreds of detainees arrested as suspected Islamic militants or their supporters have died in custody this year, some from poor conditions, others taken from their cells and shot.
In May, Jonathan said the military's emergency powers include arresting suspects, seizing buildings and "the lock-down of any area of terrorist operation." He urged the military to "take all necessary action to put an end to the impunity of insurgents and terrorists."
The Islamic extremist uprising, which began in 2009 and has killed thousands, poses the biggest threat in decades to the security and cohesion of Africa's biggest oil producer and its most populous nation. Nigeria's more than 160 million population is divided almost equally between the mainly Christian south and the predominantly Muslim north.