Fr Dhiya Azziz, a Franciscan priest serving at Yacoubieh, disappeared on 23 December as he travelled back to his church to make final preparations for Christmas.
The Custody of the Holy Land, a group which he is affiliated to, said he was returning from Turkey, where he had gone to visit members of his family who live there as refugees after fleeing Islamic State.
The 41 year old was in a taxi with other passengers when he was last heard from, the organisation said.
It added there had been no news of the whereabouts of the priest, or the others, since.
A statement said: "It is reasonable to assume that he has been kidnapped by some group. We are doing all that is possible to understand who could have kidnapped him. Unfortunately, the chaotic situation in the country does not permit us to achieve much."
Fr Azziz was held for a week by a group linked to Al-Queda in July but was released unharmed.