He said since the abducted girls were not being held in the school, the major challenge before him and his government now is to locate and rescue them.
Jonathan spoke while answering a question during a press conference held to announce the conclusions of a regional summit on security in Nigeria held in Paris, France.
The President had not visited the community since the incident happened over a month ago.
Although he was earlier scheduled to visit the school on Friday, the trip was called off later in what many people believed could have been because of security reasons.
Presidential spokesman, Reuben Abati, however said Jonathan was never scheduled to visit the town, describing the reports as malicious.
The President said during the press conference that he was not averse to visiting scenes of terror attacks as he had done so in the past.
He insisted that the Chibok case was different since there was nobody in the school.
"These girls are not held in Chibok. Sometime, people want the President to go to Chibok. If the President goes to Chibok today, it does not solve any problem. The problem facing the President and indeed the Nigerian government is how to get these girls from wherever they are," he said.
The President also noted that chiefs have already visited the area.
He also said the allegation of misappropriation of funds by the military was exaggerated but conceded that administrative lapses may have a part to play in the inadequate funding of the war against terror.
Meanwhile, the Paris summit reached several decisions that will strengthen regional co-operation.
According to the communique issued at the end of the parley, Nigeria and its neighbours will build response/analysis capabilities to enhance security of all populations.
They committed to accelerating the implementation of international sanctions against Boko Haram, Ansaru and their leaders with the United Nations framework.
All the participants also reaffirmed commitment to human rights and protection of girls who are victims of violence.
Nigeria and its neighbours resolved to embark oncoordinated patrols with the aim of combating Boko Haram and locating the Chibok girls.
They are also to establish a system to pool intelligence in order to support this operation, establish mechanisms for information exchange on trafficking of weapons and bolster measures to secure weapons stockpiles while also establishing mechanism for border surveillance.
Countries are also expected to establish an intelligence pooling unit, create a dedicated team to identify means of implementation and draw up, during a second phase, a regional counter-terrorism strategy in the framework of the Lake Chad Basin Commission.
The United States, United Kingdom, France and the European Union will coordinate their support for the regional cooperation through technical expertise, training programmes and support for the border area management programmes.
France, US, Britain and the EU pledged to mobilise donors in support of programmes fostering social economic development of the regions concerned with particular emphasis on gender equality and the rights of women and girls.
The participants agreed that the UK would host a follow up meeting next month at ministerial level to review progress on this action plan.
Chief of Defence Staff, Air Chief Marshal Alex Badeh and the National Security Adviser, Col. Sambo Dasuki (retd.), were invited into the meeting about one hour after its commencement.
Before going for the summit, Jonathan had also meet with former British Prime Minister, Gordon Brown, in his hotel room.
The Nigerian Ambassador to France, Hakeem Sulaimon, told journalists that the Paris summit was a necessary strategic forum to deal with "a very vicious terrorist group" by building regional bridge.
Sulaimon described Boko Haram as a cross-border phenomenon requiring sub-regional consensus on how to effectively tackle it.
He said, "Given the fact the fact that these terrorists resort to using safe havens by hitting and disappearing, it is important to be able to get cooperation so that specific strategic measures can be put in place including capacity to undertake hit pursuit across border lines.
"We need to be able to forge joint patrol cooperation, consolidate on joint monitoring to be able to strengthen intelligence gathering and sharing is that all countries involved will in a position to actually face the same course in addressing the problem of these plotters."
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