The order gazetted as 'Terrorism prevention and proscription order 2013' affects Boko Haram and its splinter group Ansaru, two groups known for killings and kidnappings in the oil-rich African country.
Presidential spokesman Reuben Abati yesterday explained that this action of Jonathan "officially brings the activities of both groups within the purview of the Terrorism Prevention Act and any persons associated with the two groups can now be legally prosecuted and sentenced to penalties specified by the Act".
Boko Haram and Ansaru insurgents have been attacking government structures, killing politicians, government officials, traditional rulers, soldiers, police and civilians since 2009.
Over 2,000 people have been killed by their activities.
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Recently, Jonathan declared a state of emergency in three states of Adamawa, Borno and Yobe where the terror groups are known to be more effective in their killing operations.
Nigerian army moved in to the states and forcefully took over the camps where the groups organised themselves from, especially in Borno state and also released women and children they had as captives.
Boko Haram, a major terrorist group in Nigeria, wants to install an Islamic caliphate in the oil-rich African country with a population of 150 million people equally shared between the two major religions, Islam and Christianity.