The military will take "all necessary action" to "put an end to the impunity of insurgents and terrorists" in Borno, Adamawa, and Yobe, he said.
Mr Jonathan also ordered more troops to be sent to the north-eastern states.
Militants from Boko Haram have been blamed for most of the violence, which has left 2,000 people dead since 2010.
The Islamist group, whose name means "Western education is forbidden" in the local Hausa language, is fighting to overthrow the government and create an Islamic state in the north.
Nigeria - a multiethnic nation of more than 160 million people - is also affected by a spate of conflicts over land, religion and oil.
In the latest violence, 53 people were killed and 13 villages burnt in central Nigeria`s Benue state on Tuesday.
The conflict, which started last week, is said to have been caused by a dispute over land ownership between cattle herders and farmers.
Nigerias president declares emergency
15 May 2013
Read: 833
Nigerian President Goodluck Jonathan has declared a state of emergency in three states after a series of deadly attacks by Islamist militant groups.
