He claimed some of members of the group, which had claimed responsibility for the killings in parts of the North, were in the executive, legislative and judiciary arms of government as well as the police and armed forces.
Jonathan spoke during an inter-denominational service to mark the 2012 Armed Forces Remembrance Day.
He said the situation had made it more difficult to combat Boko Haram.
The President described the current security situation in the country as worse than the civil war experience.
He said, “This is a particular time when the country has major security challenges. There are explosions every day, people are dying and are being killed daily without any reason.
“It is a period we also call on the armed forces, including those that have retired to hang with their colleagues that are still in service and government to see how collectively we can protect our nation.
“I believe we will overcome our immediate challenges. The situation we have in our hands is even worse than the civil war that we fought.
“During the civil war, we knew and we could even predict where the enemy was coming from, you can even know the route they are coming from, you can even know what calibre of weapon they will use and so on.
“But the challenge we have today is more complicated. I remember when I held a meeting with elders from the North-East and some parts of the North-West where the Boko Haram phenomenon is more prevalent, somebody said that the situation is bad that even if one’s son is a member, one will not even know.
“That means that if the person will plant a bomb behind your house you won’t know.
“Some of them are in the executive arm of government, some of them are in the parliamentary/legislative arm of government while some of them are even in the judiciary.
“Some are also in the armed forces, the police and other security agencies. Some continue to dip their hands and eat with you and you won’t even know the person who will point a gun at you or plant a bomb behind your house.”
The Primate of the Church of Nigeria, Anglican Communion, Most Rev. Nicholas Okoh, in his sermon titled ‘Patriotism at its Height’, said as the nation was passing through trying times, the total loyalty of members of the armed forces remained the only asset available to the President.
Okoh said corruption and insecurity persisted in the country, because major gladiaters lacked patriotism zeal.
“I assure Nigerians that we shall get over it. We are meeting every day and we are planning. We are going to increase the strength and the capacity of the security services to confront the modern challenges we face.”
The President identified greed and selfishness as what he called the twin evil facing the country, saying corruption is only a symptom of the two.
He said only greed and selfishness would make a marketer to smuggle petrol which has been subsidised by government to neighbouring countries.
Jonathan said the two evils were not limited to government functionaries only. He reiterated his position that though Nigerians might suffer a little, the nation would get to the promised land.
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