The surprise raids targeted the headquarters of Santiago's Ecclesiastical Court and the bishop's office in Rancagua in the O'Higgins region, where 14 priests are accused of having had sexual relations with minors.
"In Chile, we are all subject to common justice," said prosecutor Emiliano Arias, who led the raid in Santiago. Cardinal Ricardo Ezzati, the archbishop of Santiago, said church officials "gave the prosecutor all the requested documentation." He added that they are "available to cooperate with the civilian justice system in all that is required."
In May, all of Chile's 30-plus active bishops offered to quit over their collective guilt in failing to protect Chile's children from priests who raped, groped and molested them. Wednesday's raids came as two leading Vatican investigators — Archbishop Charles Scicluna and Spanish Monsignor Jordi Bertomeu — are in Chile to investigate the sexual abuse of minors committed by clergy.
Scicluna and Bertomeu earlier put together a 2,300-page report that prompted Pope Francis to realize he had misjudged the Chilean situation. The two men met Wednesday afternoon with four Chilean prosecutors, including Arias and national Attorney General Jorge Abbott.
"We came basically in search of cooperation in the investigations we are carrying out with respect to abuses suffered by minors" by people linked to the church, Abbott said. "The commitment is to a greater cooperation between the institutions."
Abbott said prosecutors met some resistance in Rancagua, though they are satisfied with the information seized in both raids. He added that in the coming days prosecutors will ask the Vatican for any information it has related to the investigations.
On Monday, Francis began purging Chile's Catholic hierarchy over the avalanche of sex abuse and cover-up cases, starting with accepting the resignations of the bishop at the center of the scandal and two others. More heads were expected to roll.
A Vatican statement Monday said Francis had accepted the resignations of Bishop Juan Barros of Osorno, Bishop Gonzalo Duarte of Valparaiso and Bishop Cristian Caro of Puerto Montt. He named a temporary leader for each diocese.
Barros, 61, has been at the center of Chile's growing scandal ever since Francis appointed him bishop of Osorno in 2015 over the objections of the local faithful, the pope's own sex abuse prevention advisers and some of Chile's other bishops.
The report exposed evidence that the Chilean hierarchy systematically covered up and minimized abuse cases, destroying evidence of sex crimes, pressuring church investigators to discredit abuse accusations and showing "grave negligence" in protecting children from pedophile priests.
Those findings opened a Pandora's Box of new accusations that led Francis to become the first pope to refer to a "culture of abuse and cover-up" in the Catholic Church. The raids in Chile were reminiscent of the police search carried out in 2010 at the headquarters of the Catholic Church hierarchy in Belgium, which prompted Pope Benedict XVI to intervene and protest the "deplorable" intrusion in the Catholic Church's legal process.
Belgian police took away computers and hundreds of files amid rumors that church leaders were continuing to cover up abuse cases. The raid prompted a Catholic panel investigating abuse to shut down in protest, saying Belgian authorities had betrayed the trust of nearly 500 victims who made complaints to the panel.