It has been reported that local Christians fear Islamic extremists have abducted Father Jacques Mourad who has not been seen since travelling with a co-worker on Thursday, when two motorcycles drew up alongside his car.
The charity says that for the past 12 years Fr Mourad had been ministering to Qaryatayn's Syriac Catholic community.
Qaryatayn is a small town around 65 miles southwest of Palmyra, which was seized by Islamic State earlier in the week.
Father Nawras Sammour, the director of the Jesuit Refugee Services for the Middle East, told Aid to the Church in Need: "We still have no news of him.
"We only know that he was abducted by four men, undoubtedly belonging to a jihadist group."
He described how Fr Jacques had welcomed refugees from Palmyra who had fled their monastery near the conflict.
Fr Sammour said: "He has always helped the Syrians and has welcomed a great many Muslims into the monastery of Mar Elias."
He said Fr Jacques continued preaching in the area even though there was a threat from extremists.
Fr Sammour said priests working in the region were aware of the dangers they faced: "We priests are fully aware of the risks we run, but we cannot do otherwise than remain alongside the Syrian people, both Christians and Muslims.
"In many cases we are the only ones they have to turn to."
The director of the Jesuit Refugee Service said: "When I asked him if he was intending to leave, he told me that he would do so only if forced - otherwise he would remain with his people."
