Jonathan will instead fly directly from the capital Abuja to Paris on Friday for a regional summit to discuss the Boko Haram insurgency and wider insecurity and will not now make a stop in the northeastern village of Chibok, said one of the sources.
"The president was planning to go but security advised otherwise on the visit," said the source of the last-minute decision to cancel the Chibok visit.
Some Nigerians have criticised the government's initial response to the plight of the girls, who were abducted on April 14, and U.S. officials this week said the government had done too little to adapt to the threat posed by Boko Haram.
Jonathan asked France last week to arrange a security summit with neighbours Chad, Cameroon, Niger and Benin, and officials from the United States, Britain and the European Union to discuss a coordinated response.
Jonathan, the former vice-president, became president of Africa's most populous nation in 2010 on the death in office of his predecessor Umaru Yar'Adua and won an election the following year. Nigeria will go to the polls again next year.