It would have been the first reported visit by the president to the scene of an attack in the northeastern region that has suffered for five years the increasingly deadly assaults by Boko Haram. Jonathan, a Christian from the south, has been accused of insensitivity to the plight of the mainly Muslim northerners. Thousands have been killed over the years, and more than 1,500 civilians have died this year alone.
"This is really sad to most of us because, we all thought he would come, and we are all thinking that his coming would give us better hope for our children's freedom," said one of the parents, who had been told to gather at the burned-out remains of the school to welcome Jonathan.
"But here we are being tossed up and down, people playing with our emotions," he complained.
The Borno state governor had cut short a trip to London, arriving home hours before the president's scheduled appearance in Maiduguri, the northeastern state capital that was the base of the Boko Haram terrorist network.
Mike Omeri, director general of the government National Information Center, denied at a news conference that the president had ever planned a trip to Chibok.
Chibok community leader Pogu Bitrus had said earlier Friday that though residents had been angry at Jonathan's slow response to the girls' plight, they did not hold it against the president and considered his visit "better late than never."
Boko Haram insurgents on April 15 abducted more than 300 students from the Chibok Government Girls Secondary School. Police say 53 managed to escape and 276 remain in captivity.
Two officials in the presidency confirmed the cancellation, saying there were apparent concerns about security after news of the planned trip was leaked to the media and published on front pages of newspapers Friday. They spoke on condition of anonymity because they are not supposed to give information to reporters.
Jonathan had been expected to fly on one of his presidential jets from Abuja, the capital in central Nigeria, to Maiduguri, and then be transported by military helicopter to the town of Chibok, 130 kilometers (80 miles) to the south.
The road from Maiduguri to Chibok passes by the Sambisa Forest to which the girls first were taken. It is a known hideout of the insurgents. Soldiers say 12 troops were killed in an ambush on that road on Monday night. For its part, the Defense Ministry said instead that four soldiers were killed in a firefight on the outskirts of Chibok that night.
Some soldiers then revolted in Maiduguri, opening fire on the car of a commanding officer who came to pay respects to the bodies brought to a barracks on Tuesday, said the soldiers, who spoke on condition of anonymity because they want to keep their jobs. The Defense Ministry said the soldiers only fired into the air. The commander, who was unharmed, has been recalled.
There have been other signs that some Nigerian troops are near mutiny, complaining that they are outnumbered and outgunned by the insurgents, are not properly paid and have to scavenge for food in the bush.
The weakness of the Nigerian military was described Thursday by Alice Friend, the U.S. Department for Defense director for African affairs at a hearing in Washington.
"And so we're now looking at a military force that's, quite frankly, becoming afraid to even engage" the enemy, she told the U.S. Senate subcommittee on African Affairs in Washington. She also said "much of the funding" for Nigeria's military is "skimmed off the top" by corrupt officers in a country where corruption is endemic.
Soldiers in Nigeria have told The Associated Press that some in their ranks actually fight alongside Boko Haram, and Jonathan last year said he suspected the Boko Haram members and sympathizers had infiltrated every level of his government and military, including the Cabinet.
In January he fired all his service chiefs, followed by the defense minister.
The militants have offered to exchange the girls for detained insurgents, and threaten otherwise to sell them into slavery. British officials say Jonathan has made clear he would not negotiate a swap.
The presidency said Jonathan is traveling later Friday to Paris for a French-organized summit with leaders of Nigeria's four neighboring countries to discuss how to address the regional threat posed by Boko Haram.
The House of Assembly on Wednesday night approved Jonathan's request to extend for another six months the year-old state of emergency covering three northeastern states, one-sixth of the country. The Senate has yet to vote.
Associated Press writers Bradley Klapper and Matthew Lee contributed to this report from Washington D.C.