"It would appear that there is a systematic effort by insurgents and terrorists to destabilize the Nigerian state and test our collective resolve," Jonathan said.
Jonathan said the order will be in force in Adamawa, Borno and Yobe states. He said the states would receive more troops, though he will not remove state politicians from their posts. Under Nigerian law, the president has the power to remove politicians from their posts and install a caretaker government in emergency circumstances.
The president's speech offered the starkest vision of the ongoing violence, often downplayed by security forces and government officials due to political considerations. Jonathan described the attacks as a "rebellion," at one point describing how fighters had destroyed government buildings and "had taken women and children as hostages."
"Already, some northern parts of Borno state have been taken over by groups whose allegiance are to different flags than Nigeria's," Jonathan said.
The president later added: "These actions amount to a declaration of war and a deliberate attempt to undermine the authority of the Nigerian state and threaten (its) territorial integrity. As a responsible government, we will not tolerate this."
Since 2010, more than 1,600 people have been killed in attacks by Islamic insurgents, according to an Associated Press count. Recently, Nigeria's military has said Islamic fighters now use anti-aircraft guns mounted on trucks to fight the nation's soldiers, likely outgunning the country's already overstretched security forces.
Meanwhile, violence pitting different ethnic groups against each other continues, with clashes that kill dozens at a time. In addition, dozens of police officers and agents of the country's domestic spy agency were recently slaughtered by a militia.
One of the main Islamic extremist groups fighting Nigeria's weak central government is Boko Haram, whose name means "Western education is sacrilege" in the Hausa language of Nigeria's north.
The group has said it wants its imprisoned members freed and strict Islamic law adopted across the multiethnic nation of more than 160 million people. It has produced several splinter groups, and analysts say its members have contact with two other al-Qaida-linked groups in Africa.
The Islamic insurgency in Nigeria grew out of a 2009 riot led by Boko Haram members in Maiduguri that ended in a military and police crackdown that killed some 700 people.
The group's leader died in police custody, in an apparent killing. From 2010 on, Islamic extremists have engaged in hit-and-run shootings and suicide bombings. Recently, however, they've begun to use military-grade weapons, some of which they apparently seized from Nigerian military stockpiles.
It remains unclear how much effect Jonathan's announcement will have. In late December 2011, Jonathan declared a similar state of emergency over parts of four states, including Borno and Yobe. The extremist attacks continued despite that.
Nigeria's military and police also have been repeatedly accused by human rights activists and others of torturing and summarily killing suspects, as well as burning down civilian homes and killing civilians in retaliation for militant attacks.
The latest incident, in a fishing village in Borno state along the shores of Lake Chad, saw at least 187 people killed and there are allegations that soldiers are responsible. While the military has denied repeatedly that it attacks and kills civilians, the country's armed forces have a history of committing such assaults.
Separately on Tuesday, an official in the central Nigerian state of Kaduna said gunmen armed with assault rifles and suspected to be Hausa-Fulani cattle herders killed 11 people in a village there. And in Benue state, a government spokesman said an attack blamed on Hausa-Fulani cattle herders there killed at least 12 people.