During the meeting, Jonathan said he is considering granting amnesty to the Islamic Boko Haram sect, a move the NEF favors.
Jonathan has previously denied NEF's requests for Boko Haram amnesty, the Daily Trust said, because the sect's members have remained anonymous.
"What we discussed is that general opinion in the country is that amnesty should be factored into all effort made by government to overcome the security challenges all over the country or in most parts of the North," Ango Abdullahi, who attended the meeting, told Leadership Newspapers.
Information Minister Labarn Maku confirmed that the president has not ruled out amnesty, but has said that some further processes must be in place before the option is fully explored.
Maku said sect members would need to identify themselves before amnesty is granted.