Prosecutors said the surprise raids took place at the dioceses of Valparaiso, Chillan, Osorno and Concepcion. Images published by local media showed authorities walking out from the buildings after seizing documents.
Chilean prosecutors and police launched raids on the offices of four bishoprics on Thursday as they continued an investigation into cases of sexual abuse of minors by members of the Roman Catholic Church, the lead prosecutor's spokesman said.
Chilean prosecutor Emiliano Arias ordered the simultaneous raids in the coastal city of Valparaiso and the southern cities of Concepcion, Chillan and Osorno.
The raids were prompted by information law enforcement officials uncovered in previous searches, said Diego Alcaino, a spokesman for Arias, by text message. He said the information relates to Oscar Munoz, a top aide to Santiago's Archbishop, who faces charges over accusations of sexual abuse of at least five minors.
Munoz and his defence are due to appear in court on Friday where they are expected to ask for him to be released from protective custody, Alcaino added.
Munoz's attorney did not immediately respond to a request for comment on Thursday. Munoz has confessed to sex crimes in documents that were seized previously by Arias. Munoz's lawyer has acknowledged that some of the accusations in the documents are true but has said he will challenge some others.
The archdiocese of Concepcion said in emailed comments that law enforcement officials took statements from several Church office employees during the raid. It said that copies of some of the documents the prosecutors sought in the raid had already been handed over, but prosecutors seized the original documents.
"This archbishopric reiterates its full respect for and compliance with the law," it said.
Representatives of the dioceses of Valparaiso and Chillan declined to comment. A representative for Osorno did not immediately reply to a request for comment.
The searches are the latest in a series of raids carried out by police in Church offices in recent months, as prosecutors look for new cases of sexual abuse or evidence that Church officials concealed abuse from authorities.
Last month, the Chilean government requested that the Vatican share canonical documents related to nine clergy members accused of sex crimes.
The ongoing Church sex abuse scandal in the Andean nation has prompted Pope Francis to open an investigation that has led to the resignations of five bishops and priests.
In June, the pope accepted the resignation of Juan Barros, the former bishop of Osorno, who was accused of covering up sexual abuse by his mentor, Fernando Karadima.
Pope Francis has told Chilean Catholics affected by the sex abuse scandal that the Church will "never again" ignore victims.