Maltese archbishop Charles Slicluna was accompanied by another papal envoy Jordi Bertomeu.
"We have come to ask forgiveness" from the victims on behalf of Pope Francis, said Bertomeu as they arrived in Santiago.
The two officials are to travel to Osorno, the Catholic diocese that was led by controversial bishop Juan Barros, one of three bishops whose resignation Francis accepted on Monday, following a child sex abuse scandal which has come to haunt his papacy.
The entire Chilean delegation of bishops that was called to a meeting with the pope in the Vatican last month resigned. But so far, the pope has accepted only three resignations.
When asked if others were to follow, Bertomeu said: "That we have to leave in their hands, but we have to be very expectant that things will go very well."
Vatican orders ex-diplomat to face child sex abuse trial
Several members of the Church hierarchy, including Barros, are accused by victims of ignoring and covering up years of child abuse by Chilean pedophile priest Fernando Karadima during the 1980s and 1990s.
Francis appointed 61-year-old Barros as bishop of Osorno in 2015, when victims' allegations against him were already widely known.
And the pontiff himself became mired in the scandal when, during a trip to Chile in January, he defended Barros who was accused of covering up Karadima's wrongdoing.
Scicluna and Bertomeo visited Chile in February to investigate the allegations and meet with victims. Their report to Rome noted the existence of a "culture of abuse" within the Chilean Church.
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