The Vatican's announcement comes after an unprecedented move by all of Chile's 34 bishops, who recently offered to resign en masse after attending a crisis meeting with the pope over allegations of a cover-up of sexual abuse in the South American nation.
The Pope named apostolic administrators to run each diocese in the meantime: Mercedarian Father Ricardo Basilio Morales Galindo, Chilean provincial, for the Archdiocese of Puerto Montt; Auxiliary Bishop Pedro Ossandon Buljevic of Santiago for the Diocese of Valparaiso; and Auxiliary Bishop Jorge Concha Cayuqueo of Santiago for the Diocese of Osorno.
"We have come to ask forgiveness" from the victims on behalf of Pope Francis, said Bertomeu as they arrived in Santiago.
The investigators, Archbishop Charles Scicluna and Spanish Monsignor Jordi Bertomeu, are heading back to Chile on Tuesday to begin what the Vatican has said is a "healing" mission to Osorno.
Barros had always been accused of witnessing and covering up the sexual abuse of minors by a priest who had once mentored him.
Of the three, only one, the 61-year-old Barros, is below the retirement age of 75.
Pope Francis has, according to BBC, apologized to victims after more than 1,000 Chileans wrote to him, asking him to reconsider the installation of Juan Barros as bishop of the Chilean city of Osorno.
Scicluna is due to return to Chile this week to gather more information.
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He also chose to host three Chilean sex abuse survivors at his home in the Vatican so he could apologise to them personally and hear their recommendations for change.
In a letter to Chileans released at the end of last month, the pontiff voiced "shame" that the Catholic Church failed "to listen and react in time" to the allegations of sexual abuse by Chilean clergy.
Karadima, a charismatic cleric who was a mentor for Barros and other priests, was sentenced by the church in 2011 to a lifetime of penance and prayer for the sex crimes he is accused of.
Barros, who is a central figure in the controversy, has been accused of covering up abuse committed by another priest in the 80s and 90s.
That same month he received at the Vatican three Chilean whistleblowers in the sexual abuse case.
A Vatican official said that Monday's move represented a first step towards re-ordering the battered Roman Catholic Church in Chile and that the pope was still considering the positions of the other prelates.
Francis has apologised to the victims and admitted he had made "grave mistakes" after reading a 2,300-page report on abuses in Chile.
"I told him that Barros was watching us when we were abused, I think that's clear to him now", Juan Carlos Cruz said.