Francis also faced controversy on another front: Overnight three more Catholic churches were torched, two in the southern Araucania region where Francis will visit on Wednesday to meet with Chile's indigenous peoples.
While not causing any injuries, the nine church firebombings in the past few days have marked an unprecedented level of protest against history's first Latin American pope on his home turf.
In his first event of the day, Francis met privately with Chilean President Michelle Bachelet and addressed lawmakers, judges and other authorities at La Moneda palace. They interrupted him with applause when he said he felt "bound to express my pain and shame" that some of Chile's pastors had sexually abused children in their care.
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Francis didn't refer by name to Chile's most notorious pedophile priest, the Rev. Fernando Karadima, who was sanctioned in 2011 by the Vatican to a lifetime of "penance and prayer" for sexually molesting minors. Nor did he refer to the fact that the emeritus archbishop of Santiago, a top papal adviser, has acknowledged he knew of complaints against Karadima but didn't remove him from ministry.
While the scandal rocked the church, many Chileans are still furious over Francis' subsequent decision, in 2015, to appoint a Karadima protege as bishop of the southern city of Osorno. Bishop Juan Barros has denied knowing about Karadima's abuse but many Chileans don't believe him, and his appointment has badly split the diocese.