"I apologize to all those I have offended and I hope to be able to do it personally in the coming weeks, in the meetings I will have" with victims, he said in a letter to Chilean bishops.
Following the release of Pope Francis' letter, Bishop Santiago Silva Retamales, president of the bishops' conference and head of the military ordinariate, said the bishops of Chile would travel to the Vatican in the third week of May.
In a letter to 32 Chilean bishops released by the Vatican, Francis said he meant to summon them to Rome to discuss an investigation into an alleged cover-up by Bishop Juan Barros of abuse by paedophile priest Fernando Karadima during the 1980s and 1990s.
Francis' decision to send Archbishop Scicluna to Santiago to investigate the accusations came after controversy flared during the pope's January 15-18 visit to Chile, during which he responded to a Chilean journalist who asked about the Bishop Barros issue, saying the accusations were "calumny", because there was no proof.
Many have accused Bishop Barros of having witnessed abuse when he was young and failed to report Karadima.
Karadima, an influential Chilean priest, was convicted by the Vatican in 2011 of abusing teenage boys and sentenced to a life of penitence.
The letter comes after a March report detailing interviews with 64 people affected by the scandal.
Apologies have not been enough to calm the victims of the Catholic Church's sexual abuse scandal - at least not the kind of apologies the pope has been willing to offer. There is not one piece of evidence against him.
"The day they bring me proof against Bishop Barros, I'll speak". It is all slander.
On the plane returning from Chile, Francis told reporters he believed the bishop was innocent. "Is that clear?" the pope replied.
Other clerics more favorable to Barros had Francis' ear, such as the Vatican ambassador, who has always been hostile to Barros' accusers. "Archbishop Scicluna did an excellent job with his investigation", Ms Collins added.
But the Chilean bishops insisted they had been truthful to Francis about the need to get rid of Barros - they had proposed he resign and take a year sabbatical - and victims' advocates said Francis had only himself to blame, since the accusations against Barros were well known and well-founded.
However, he admitted "obviously we didn't do everything we should have done".
In words that laid bare his simmering anger, Francis said they must now work together to "re-establish confidence in the church, confidence that was broken by our errors and sins, and heal the wounds that continue to bleed in Chilean society".
Pope Francis said he wanted to meet with the bishops to discern immediate and long-term steps to "re-establish ecclesial communion in Chile in order to fix the scandal as much as possible and re-establish justice". Still, they said specific measures, including the resignation of Barros, were needed to restore confidence in the Church. He also said they should present "proof" of their claims.
Such gatherings are rare and usually take place in a period of crisis in a national Church, such as when the USA paedophile priest scandal broke in 2002.
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