The incident in Jonesborough village in south Armagh unfolded late last night when the cleric found three youths in his office.
They attacked him and bundled him into the bathroom, locking the door behind them before making off with a sum of cash.
The priest eventually managed to escape from the room by climbing out of the window.
He was taken to hospital for treatment to facial injuries.
Police have urged anyone who noticed anything suspicious in the area at around 11.30pm to come forward.
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