The Saltillo Catholic Diocese in northern Mexico said in a statement that the body of Fr Joaquin Hernandez Sifuentes had been discovered.
Fr Sifuentes was a parish priest in the state of Coahuila, an area plagued by drug cartel violence.
The priest was scheduled to take a holiday but his friends were unable to contact him after 3 January.
A neighbour reported seeing two men take Fr Sifuentes' car but did not see the priest with them.
Mexico
Population: 122 million
Christian population: 120 million (82 per cent Catholic)
Mexico is ranked 41st on the Open Doors watchlist for Christian persecution 2017
The country has a long history of anti-clericalism and in the past century the government officially and often violently suppressed church leaders
A friend then visited the priest's residence and found his room ransacked. His packed suitcase and glasses were found in the room.
The Coahuila state Prosecutor's Office said in a statement that the body was found in the town of Parras de Fuente. An autopsy will be performed to determine the cause of death.
The Saltillo Diocese said: "Fr Joaquin was someone who looked for perfection in everything he did; the desire to always innovate in his work, has been reflected in love by the faithful, including during the past 10 days."
At least 32 Catholic priests have been murdered in Mexico since 2006.
Mexico's Catholic Media Centre says the country is the most dangerous in the world to be a priest.
The US State Department wrote in its 2015 International Religious Freedom report that priests in Mexico are "victims of extortion attempts, death threats, and intimidation by organised criminal groups."