The Rev. Alejandro Solalinde has endured death threats after publicly denouncing drug gangs and police who rob and kidnap the mainly Central American migrants who cross Mexico seeking to reach the United States.
Solalinde says the bishop of his diocese in southern Mexico has told him he was gaining too much attention with his public complaints and wants to reassign him to parish duties.
The priest said Wednesday he will ask church authorities to assign him to another migrant shelter.
The bishop's office did not immediately respond to requests for comment.
In May Solalinde said he was leaving Mexico temporarily for his own safety.
"The situation is very delicate and that's why it's necessary to take a short break ... and I am not leaving due to fear. If that was it, I would keep quiet," Solalinde said in a press conference, according to EFE.
The Catholic priest founded the Hermanos del Camino shelter in the southern state of Oaxaca, where some 200 Central American migrants arrive each day.
Amnesty International recently said Solalinde had received death threats and called on Mexican officials to protect him and the migrants he assists.
Two individuals stopped Solalinde on April 15 as he was guiding about 1,500 migrants to the shelter he runs in Ixtepec, a city in Oaxaca, and started harassing him, Amnesty International's Mexico office said.
"When the priest intervened, the two men insulted him and threatened to kill him," the human rights group said.
A person working with Solalinde revealed that information had been received that a hit man had been hired to kill the Catholic priest, Amnesty International said.
An estimated 300,000 Central Americans undertake the hazardous journey across Mexico each year on their way to the United States.
The trek is a dangerous one, with criminals and corrupt Mexican officials preying on the migrants.
Gangs kidnap, exploit and murder migrants, who are often targeted in extortion schemes, Mexican officials say.
A total of 46,716 Central Americans were deported from Mexico between Jan. 1 and Nov. 30, 2011, the National Migration Institute, or INM, said in a report released earlier this year.