"On the night of October 5th, Father Hanna Jallouf of the Custody of the Holy Land, parish priest at Qunyeh, Syria, was taken by some brigades linked to Jabhat Al-Nusra," a statement from the Custody of the Holy Land said.
Following their capture, an unspecified number of Franciscan nuns had taken refuge with the villagers, it said.
Qunyeh is a village of several hundred people in Idlib province, and lies some eight kilometres from the Turkish border.
"He has been kidnapped," he told AFP in Jerusalem, expressing deep concern over the fate of the priest, a Syrian who has worked in Qunyeh for 12 years after a posting in the Jordanian capital, Amman.
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"They are accusing them of being collaborators" with the regime of Syrian President Bashar al-Assad, he said, insisting that this was not true.
"We don't know what to do. We don't know with whom to talk, we're totally unable to get in touch with anyone," added Pizzaballa, the guardian of the Catholic Church's sites in the Holy Land.
He also said Al-Nusra rebels were "angry with Father Hanna because he refused to give them some of the olives harvested from trees on the convent's land."
Pizzaballa could not confirm reports that the convent had been plundered, saying the claim was being looked into.
Contacted online by AFP, a local Syrian activist said Al-Nusra had been trying to take charge of part of the Franciscan properties in Qunyeh, prompting Father Hanna to make a complaint to a religious court late last week.
The Franciscans, a religious order within the Catholic Church, have 19 people working across Syria, where the order has operated for 800 years. They have been working in Qunyeh for 125 years, he said.
The Custody of the Holy Land is made up of 285 members of the Franciscan Order from 39 countries.
Al-Nusra Front, which fights alongside rebels battling Assad's regime, is the Syrian branch of Al-Qaeda.