In a national broadcast, Jonathan declared a state of emergency in Borno, Yobe and Adamawa states, saying the country will stand firm "against those who threaten the sovereign integrity," the Daily Trust reported Wednesday.
"Our will is strong, because our faith lies in the indivisibility of Nigeria," Jonathan said Tuesday.
Security officials told the Daily Trust a large-scale military deployment started before the proclamation. At least 8,000 troops were expected to be deployed.
Jonathan said he decided to declare a state of emergency in the three states because insurgents' activities amounted to a declaration of war on the nation.
Despite "robust steps" to end the insurgency, it appears "there is a systematic effort by insurgents and terrorists to destabilize the Nigerian state and test our collective resolve," Jonathan said.
"What we are facing is not just militancy or criminality, but a rebellion and insurgency by terrorist groups which pose a very serious threat to national unity and territorial integrity," he said. "Already, some northern parts of Borno state have been taken over by groups whose allegiance is to different flags and ideologies."
The emergency declaration directs the defense minister to deploy more troops to the three states immediately, the Daily Trust said. Governors and other officials in the affected states will remain in office, the Daily Trust said.