He ordered closure of all land and sea borders in the affected areas. Jonathan during a nationwide broadcast declared a state of emergency in five local government areas of Borno state, five local government areas of Yobe state, four local government areas of Plateau state and one local government area of Niger state.
Meanwhile, a blast followed by a shootout near a mosque claimed four lives as suspected militants of a radical group launched an attack in the troubled northern Nigerian city of Maiduguri.
He said the chief of defence staff and the inspector general of the police force would take necessary actions concerning the affected areas while he announced the setting up of a counter-terror group within the armed forces to handle the issues of terrorism in the region.
"As part of the overall strategy to overcome the current security challenges, I have directed the closure of the land borders contiguous to the affected Local Government Areas so as to control incidences of cross boarder terrorist activities as terrorists have taken advantage of the present situation to strike at targets in Nigeria and retreat beyond the reach of our law enforcement personnel," he said.
Before the state of emergency announcement, Jonathan had paid a visit to Madalla town, near the federal capital territory, Abuja where the sect threw bomb on Christmas day on churchgoers killing not less than 44.
The total number of deaths resulting on simultaneous attacks on other northern cities on the Christmas day has been put at 49. He had described the sect as "cancerous" and lamented that any attack on any part of the nation is "an attack on all of us".
The activities of the Boko Haram has raised fears of religious conflict in the country since the Christmas day bombing as the Christian Association of Nigeria (CAN) which sees the attack as directed at its members has warned of retaliation.
Jonathan also held a meeting with his security chiefs in which he told them to take urgent steps to stop the threats posed by the sect. On Tuesday, a top Islamic leader appealed for calm after a crucial meeting with the president.
Muhammad Saad Abubakar, the Sultan of Sokoto caliphate met with President Goodluck Jonathan and said "good people must come together to defeat the evil ones".
Boko Haram sect has been waging a bloody conflict to install an Islamic government and Sharia rule in the country. A suicide bomb attack by the group at the United Nations headquarters in Abuja in July killed 26 persons.
The 150-million Nigeria has both Muslim and Christian population, with Muslims predominant in the north while Christians mostly live in the South.