The move came as Vatican investigators met with Chile's attorney general to discuss co-operation into ongoing probes.
The surprise raids targeted the headquarters of Santiago's Ecclesiastical Court and the diocese in Rancagua in the O'Higgins region, where 14 priests are accused of having had sexual relations with minors.
They came hours before two envoys sent by Pope Francis met with Chilean prosecutors, including attorney general Jorge Abbott, to co-ordinate their response to scandals that have discredited Chile's church.
Last month all of the country's 30-plus active bishops offered to resign over their collective guilt in failing to protect children from abusive priests.
"The commitment is to a greater collaboration between the institutions," said Mr Abbott.
He added that church and civilian authorities are going to set up a system that will provide victims with the protection needed to come forward and freely lodge complaints.
Mr Abbott said prosecutors met some resistance in the Rancagua raid, though they were satisfied with the information seized in both operations.
He added that in the coming days prosecutors will ask the Vatican for any information it has related to the investigations.
Cardinal Ricardo Ezzati, the archbishop of Santiago, said church officials "gave the prosecutor all the requested documentation".
He added that they are "available to co-operate with the civilian justice system in all that is required".
Prosecutor Emiliano Arias, who led the search in Santiago, said the church raids show that in Chile "we are all subject to common justice".
The Vatican investigators in Chile - Archbishop Charles Scicluna and Spanish Monsignor Jordi Bertomeu - had earlier put together a 2,300-page report that prompted Pope Francis to realise he had misjudged the Chilean situation.
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 centre of the scandal and two others.
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