Juan Barros has been ordained bishop in the Chilean city of Osorno despite being widely accused of covering up crimes of a Catholic reverend who the Vatican sanctioned for sexually abusing young boys.
Barros was appointed on Saturday, as hundreds protested against the move outside the church hosting the ceremony.
Demonstrators dressed in black, a symbol of mourning, denounced the 58-year-old and many called for him to immediately resign.
Police had to escort Barros out of the church after his ordination, which was attended by only 15 of the country's 35 bishops and about 20 of the 35 priests in the diocese some 930km south of the capital Santiago.
While Barros himself is not accused of molestation, at least three victims of sex abuse say he was present when they were molested by the Reverend Fernando Karadima in the 1980s and 1990s.
The controversy has been closely watched by victims, advocacy groups and politicians as a test of Pope Francis' promises to crack down on clerical sex abuse.
"I hold the pope responsible," said Juan Carlos Cruz, a 51-year-old journalist who is one of the accusers.
"As victims, we had become used to the slaps in the face by the Chilean hierarchy, but we never expected a slap in the face from the pope," he told the AP news agency.
Barros had long declined to comment publicly on the allegations against him. However, he sent a letter to priests in the diocese on Monday saying he did not know about Karadima's abuses when they happened.
"I never had knowledge of, or could have imagined, the serious abuses that this priest committed against the victims," said the letter.
The pope confirmed his decision to appoint Barros after he recently met with him.
More than 1,300 church members in Osorno, along with some 30 priests from the diocese and 51 of Chile's 120 congress members sent letters to Francis in February urging him to rescind the appointment.
A Vatican investigation found Karadima, one of Chile's most prominent priests, guilty of sex abuse in 2011 and sentenced the now 84-year-old priest to a cloistered life of "penitence and prayer".
Criminal charges against him were thrown out because the statute of limitations had expired.
Cruz said that he and another teenage boy would lie down on Karadima's bed, one resting his head at the man's shoulder, another sitting near his feet. The priest would kiss the boys and grope them, he said, while Barros watched.