The case marks the first time the Catholic Church in Mexico has turned a priest in to authorities.
The move follows instructions from Pope Francis for the Catholic Church to better protect children and take a hard line with priests accused of sexual offenses.
Father Eduardo Cordova Bautista, a priest in the Archdiocese of San Luis Potosi, was ordered in late April by the Vatican to face charges for allegedly abusing a 16-year-old boy in 2012. The actions were implemented in late May. His whereabouts were unknown, however.
"This is simply acting on a petition of the pope and what he's asking: that we collaborate completely with the judicial system," said Armando Martinez Gomez, president of the College of Catholic Lawyers of Mexico.
The case of Cordova created a scandal in Mexico after journalist Sanjuana Martinez reported earlier in May that dozens of youth were allegedly abused by the priest over the past 25 years as he worked in Catholic institutions serving young people.
Alberto Athie, a former priest and an early accuser of the disgraced Father Maciel Marcial Degollado, founder of the Legionaries of Christ, said there may be as many as 100 victims, Diario de San Luis reported.
The actions taken against Cordova mark a change in Mexico, where cases of clerical abuse have often languished while dioceses have been slow to act.
"What I know is this is the first time in which there was a canonic procedure and a public complaint. This is not something to be proud of," Armando Martinez Gomez told Desde la Fe.
"These news stories are always sad, but they have to be an example that the church does not tolerate nor will it tolerate this type of conduct, much less when it is has now been proven, in this case, by an Ecclesiastical Tribunal," he said.