"The president has cancelled his visit to Chibok. It was on his schedule up until this morning," a presidential official told AFP, without giving a reason.
Instead of visiting the remote town in northeastern Borno state, Jonathan is now due to head direct to a security summit in Paris tomorrow to discuss the Boko Haram threat to regional stability.
Nigeria's government and Jonathan in particular have been heavily criticised for their slow response to the kidnapping on April 14, which saw Islamist militants snatch 276 girls from their school.
A total of 223 are still missing and the group's leader, Abubakar Shekau, claimed in a video released this week that some 130 had now converted to Islam.
A social media campaign has galvanised international pressure on Nigeria to mount a rescue operation and the United States, Britain, France and Israel have all sent teams and equipment to help.
But his cancellation, reportedly over security concerns in the troubled northeast, will likely prompt further criticism of the government's handling of the crisis.
The United States said yesterday condemned Nigeria's "slow" response to the kidnapping and said resolving the crisis was not "one of the highest priorities of the US government".
Debo Adeniran, of the Coalition Against Corrupt Leaders pressure group, said he was "shocked and disappointed" at the cancellation of the belate visit -- and it sent a troubling message.
"If as the commander-in-chief of the armed forces, he is afraid to visit Chibok because of security fears, he is simply telling the hapless people in the northeast that he cannot protect them and they should resign to their fate," he said.
"He is also telling the soldiers fighting Boko Haram elements in the region that they are on their own," he added, calling for Jonathan to resign.