In a televised address to the nation, Jonathan declared a "state of emergency in Adamawa, Yobe and Borno states".
In the address after two days of meetings with security chiefs, Jonathan said it has become obvious that members of the Boko Haram Islamic militant group and other sects were bent taking over some parts of Nigeria.
"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.
He did not remove the governors of the three states but ordered security forces to pay closer attention to the areas.
Boko Haram has killed more than 2,000 people since it started insurgency in 2009. It concentrates its activities in the three states where the emergency was declared with frequent shift to neighbouring states.
Recently a breakaway sect, Ansaru and a cult, Ombatse joined in the attacks and killings. On Thursday, Ombatse opened fire on police officers during an ambush in Nasarawa state, killing 30 of them.