This is contained in a statement issued by the Special Adviser to the President on Media and Publicity, Dr Reuben Abati from N'Djamena.
The statement said that Jonathan made the call while speaking to reporters at the Presidential Palace in N'Djamena after a closed-door meeting with his Chadian counterpart, President Idris Deby.
Jonathan was quoted as saying that their talks focused mainly on security and economic cooperation.
According to the statement, the president told reporters that Boko Haram had a lot of external influence from outside Africa.
He said that this had made it even more imperative for all countries in the region to work together to overcome terrorism and other criminal activities across their borders.
``If you look at the economies of Nigeria and Chad, both are linked. The Boko Haram people don't take permission to move from Chad, Niger, Cameroon and Nigeria.
``If the countries do not cooperate, we will not find it easy to win the war, because when the heat is strong in one country, the criminals and terrorists will go to another one and hide.
``So, we must work together and we are discussing along that line,'' the statement quoted him as telling reporters.