The Islamist insurgents, who say they are fighting to create an Islamic state in the north, have carried out scores of attacks since 2009 but Jonathan said the violence can no longer be treated as "militancy or criminality".
In a televised speech on Tuesday, he described the attacks as amounting to "a rebellion and insurgency by terrorist groups which pose a very serious threat to national unity and territorial integrity."
The president for the first time acknowledged that parts of Borno state, the epicentre of the Boko Haram conflict, have been "taken over" by insurgents with Nigeria's sovereignty having been displaced.
"I hereby declare a state of emergency in Borno, Yobe and Adamawa states," Jonathan said, referring to the three northeastern states which have been among the hardest hit.
He said more troops would "immediately" be deployed to the areas.
Jonathan made a similar move in January 2012 following a spate of Boko Haram attacks, but in that case the decree only applied to specific local government areas in four states.
In seeking to impose the measure across a whole state, Jonathan must first secure the approval of Nigerian legislators, which he pledged to do.
The enhanced powers that come with the measure are unclear.
When former president Olusegun Obasanjo invoked the measure twice in 2004 and 2006, he removed democratically elected governors and installed appointed administrators to manage the states, both former military officers.
Jonathan vowed that he would not employ that measure.
"The governors and other political office holders in the affected states will continue to discharge their constitutional responsibilities," he said.
The troops being sent to the three states will be authorised to seize buildings, lock down neighbourhoods and conduct sweeping searches, the president said, but those tactics have already been widely used by the security forces.
The Boko Haram insurgency has cost some 3 600 lives since 2009, including killings by the security forces.
But a series of recent brazen attacks have raised concerns that insurgents have become emboldened, with Jonathan saying that the latest violence amounted to "a declaration of war".
On May 7 in northern Borno state, suspected Boko Haram gunmen stormed the town of Bama in a convoy of seven vehicles and staged co-ordinated attacks on the military and police, killings dozens.
Jonathan has faced mounting pressure over his struggles to stem the violence and launched a bid to offer the insurgents amnesty after key Islamic leaders backed the move.
The president said this "multi-track" approach involving "persuasion, dialogue and widespread consultation", would continue but explained that the unchecked violence of the militant groups had forced him to pursue more aggressive measures.
"We will hunt them down, we will fish them out," he said of those collaborating with the rebellion.
Nigeria is Africa's most populous country with an estimated 160 million people, including a mostly Christian south and predominately Muslim north. – AFP