Father Jose Luis Sanchez Ruiz had last been seen on Thursday, and the next day the doors to his church in Catemaco, a town in the eastern state of Veracruz, had signs of forced entry.
His disappearance sparked fears that he had suffered the same fate as two other priests who were found dead in Veracruz in September shortly after their disappearance.
But the archdiocese of San Andres Tuxtla said in a statement that Sanchez Ruiz, 54, was found on Sunday morning "with notable signs of torture."
Sanchez Ruiz had received threats after complaining about crime in Catemaco.
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Mexico is one of the most violent places for priests in the world.
In September, two priests were found dead on the roadside a day after they were taken away from their church in another town in Veracruz. Prosecutors have detained two people and say the priests were killed by acquaintances after an argument.
That same month, another priest was found shot dead after disappearing in the western state of Michoacan.