Scicluna is due to return to Chile this week to gather more information.
Francis apologized to the victims and admitted he had made "grave mistakes" after reading a 2,300-page report on abuses in Chile.
Abuse survivors have alleged that when Bishop Barros was still a priest he witnessed their abuse by his mentor, Fr Fernando Karadima. Joining him is Marie Collins, an Irish survivor of abuse who resigned from O'Malley's panel previous year in frustration over the Vatican's resistance to listening to victims.
The installation of Juan Barros as bishop of the southern city of Osorno in 2015 met with stiff resistance.
"Today begins a new day for the Catholic Church in Chile and hopefully the world", Cruz wrote.
"The day I see proof against Bishop Barros, then I will talk".
The scandal and fury over the bishop cast a dark shadow over Francis' visit to Chile earlier this year: At least five churches were attacked in Santiago -some with firebombs - and a death threat was made against the pope.
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But by also accepting the resignations of the two other bishops, Francis is making clear that the troubles in Chile's church do not rest on Barros's shoulders alone, or on those of the more than 40 other priests and three other bishops trained by Fernando Karadima.
Bishop Juan Barros looks on as Pope Francis leaves at the end of a mass at the Lobito beach in Iquique, Chile January 18, 2018.
The Vatican in 2011 sentenced Karadima, a powerful preacher close to Chile's elite, to a lifetime of penance and prayer for his sex crimes. But the Scicluna-Bertomeu report exposed a far bigger scandal that has implicated several religious orders, including priests and brothers in the Franciscans, the Legion of Christ, the Marist Brothers and the Salesian orders.
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.
An worldwide family rally the Catholic Church is hosting in Ireland will feature workshops on hot-button issues facing Catholic families, including protecting children from clergy sexual abuse, weathering divorce and ministering to lesbian and gay faithful. To date, 14 priests in Rancagua have been suspended and the bishop resigned as head of the commission after admitting he was slow to act on accusations that a minor had been abused.
Jaime Coiro, general secretary of the Chilean Catholic Church, noted that the pope has said the case will require short-, medium- and long-term measures, which could include accepting the resignations of more bishops. He called for a process to find "truth, justice and reparation" for the damage caused. At the time he said that allegations against the bishop amounted to "slander".