Pope Francis met with survivors of priests who sexually abused them, wept with them and apologised for the “irreparable damage” they suffered, his spokesman said.

The pontiff also acknowledged the “pain” of priests who have been held collectively responsible for the crimes of a few, Vatican spokesman Greg Burke told reporters on Tuesday, during Francis’ first visit to Chile.

Francis dived head-first into Chile’s sex abuse scandal on his first full day in Santiago that came amid unprecedented opposition to his visit: three more churches were torched overnight, including one burned to the ground in the southern Araucania region where Francis celebrates Mass on Wednesday.

Police used tear gas and water cannons to break up an anti-pope protest outside Francis’ big open-air Mass in the capital, Santiago.

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Inmates reach out to Pope Francis as he visits the San Joaquin women’s prison in Santiago (Alessandra Tarantino/AP)

Despite the incidents, huge numbers of Chileans turned out to see the pope, including an estimated 400,000 for his Mass, and he brought some inmates to tears with an emotional visit to a women’s prison.

But his meeting with abuse survivors and comments in his first speech of the day were what many Chileans, incensed by years of abuse scandal and cover-up, were waiting for.

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A banner reading “Francis, accomplice of paedophile crimes” is displayed in Santiago (Victor Caivano/AP)

Mr Burke said Francis met with a small group of abuse victims after lunch, listening to their stories and praying with them. The spokesman gave no details, other than to say the pope “listened to them, prayed with them and wept with them.”

Earlier in the day, Francis told Chilean President Michelle Bachelet, politicians, judges and other authorities that he felt “bound to express my pain and shame” that some of Chile’s clergy had sexually abused children in their care.

“I am one with my brother bishops, for it is right to ask forgiveness and make every effort to support the victims, even as we commit ourselves to ensuring that such things do not happen again,” the pope said.

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Nuns express their happiness as Pope Francis walks past as he arrives at the Cathedral, in Santiago (Alessandra Tarantino/AP)

Francis did not refer by name to Chile’s most notorious paedophile priest, the Reverend Fernando Karadima, who in 2011 was barred from all pastoral duties and sanctioned 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 Mr Karadima but did not remove him from ministry.

“Sex abuse is Pope Francis’ weakest spot in terms of his credibility,” said Massimo Faggioli, a Vatican expert and theology professor at Villanova University in Philadelphia.

“It is surprising that the pope and his entourage don’t understand that they need to be more forthcoming on this issue.”

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Pope Francis blesses a pick up truck that used to belong to St. Alberto Hurtado, during a visit to his shrine (Natacha Pisarekno/AP)

Anne Barrett Doyle, of the online abuse database, BishopAccountability.org, praised Francis for opening his visit with the apology, but said Chileans expect him to take action against complicit church leaders.

“This is a crucial opportunity for Francis. With luck, he will not make the mistake of his brother bishops in underestimating the savviness and moral outrage of the Chilean people,” said Ms Barrett Doyle, who last week released research showing nearly 80 Chilean priests have been credibly accused or convicted of abuse.

The Karadima scandal and long cover-up has caused a crisis for the church in Chile, with a recent Latinbarometro survey saying the case was responsible for a significant drop in the number of Chileans who call themselves Catholic, as well as a fall in confidence in the church as an institution.