The president said only the physical appearance of the leadership of the group in person could change this stand.
Recently, a prominent traditional leader in the northern part of the oil-rich African country, the Sultan of Sokoto, Abubakar Sa'ad had requested for an amnesty for the group which has been carrying out killings since 20009.
"Even though the federal government is desirous of ending the spate of violence occasioned by the group's belligerence, it cannot declare amnesty for ghosts."
"We cannot talk about amnesty for the Boko Haram now until you see the people you are dealing with," he said.
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Yobe is close to Maiduguri, a stronghold of terror group Boko Haram and has witnessed series of attacks.
The sect has killed thousands of people since it waged a war against the Nigerian state in 2009 in an attempt to establish an Islamic caliphate in the country.
Nigeria has a population of 150 million people divided equally by the two predominant religions, Islam and Christianity.