But several militant indigenous groups see the Roman Catholic Church as being closely associated with the history of oppression, and they have staged arson attacks against churches in the region. In November, hooded activists set fire to a bus and scattered pamphlets after the pope’s visit to the region was announced.

The pamphlets left outside the churches in Santiago on Friday were not entirely coherent. They referred to “dominion over our bodies,” and included the phrase “free, impure and savage bodies,” suggesting criticism of the church’s conservative social positions on sexuality and abortion.

They also called for freedom for “political prisoners all over the world,” and contained a threat against the pope.

“We attack with the fire of combat, exploding your disgusting morals,” it said. “Pope Francis, the next bombs will be on your robe!”

After visiting the churches that were attacked, Archbishop Ricardo Ezzati of Santiago said, “We are deeply hurt by these events that contradict the spirit of peace that inspires the pope’s visit.”

President Bachelet, who is scheduled to leave office in March, condemned the attacks. “In a democracy people can express themselves, as long as it is in a peaceful and adequate manner,” she said.

Pope Francis is to arrive in Santiago on Monday night. On Tuesday he will celebrate Mass at a major public park and meet with Ms. Bachelet, government officials, members of the diplomatic corps and Chilean bishops. He will go to Temuco the following day and then visit the northern city of Iquique on Thursday morning before flying to Lima, Peru.

In addition to the Mapuche, another source of controversy around the visit is the issue of the complicity of Chilean bishops in the case of the Rev. Fernando Karadima, the former head of El Bosque parish in Santiago, who catered to the elite while abusing teenage boys. The Vatican found Father Karadima guilty of sexual abuse in 2011 and sentenced him to a life of penitence and prayer. The church sentence was the only punishment leveled against the abusive priest. Victims were unsuccessful in an effort to get compensation through civil litigation. But no actions have been taken against the tight circle of bishops whom he trained, and who victims say covered up his crimes.

In January 2015 Pope Francis appointed one of them, Juan Barros, as bishop of Osorno, 570 miles south of the capital, prompting protests by lay and religious groups that continue to this day.

On Thursday, The Associated Press revealed a letter sent by Pope Francis to Chile’s Bishop’s Conference that same month after they expressed concern over the appointment. Francis told them that he had planned to offer a sabbatical to Bishop Barros and two other bishops with ties to Father Karadima in order to cool the heated environment over his controversial appointment. That move ultimately failed.

Father Karadima’s victims criticized the pope for not making time to meet with them during his visit, as they requested months ago.

“There has been no evidence that Pope Francis has done anything to support his stated zero-tolerance policy on abuses,” said James Hamilton, one of Father Karadima’s victims. “We would have expected at least action against the bishops complicit with Karadima.”

This week the organization BishopAccountability.org published research showing that almost 80 members of the clergy in Chile have been accused of sexual abuse since 2000. More than half have been convicted in court or by the Vatican.

Francis arrives in the midst of legislative debate over a gender identity bill that had been scheduled for debate in the lower house of Congress on Tuesday. The president of the Chamber of Deputies, Fidel Espinoza of the Socialist Party, postponed the debate in deference to the church.

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