Prosecutors and police earlier in the day raided the office of the bishop of Rancagua, south of the capital, to seize documents.
The raids led by prosecutor Emiliano Arias targeted the headquarters of Santiago's Ecclesiastical Court and the bishopric of Racagua, where 14 diocese priests are accused of having had sexual relations with minors.
Scicluna and his colleague Father Jordi Bertomeu, a Spanish official from the Vatican, arrived in Chile on Tuesday with orders from Pope Francis to ensure the Church responds to "every case of sexual abuse of minors committed by clergymen". He added that they are "available to cooperate with the civilian justice system in all that is required".
Papal envoys Archbishop Charles Scicluna and Msgr Jordi Bertomeu are on their second visit to Chile to take statements from victims.
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.
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Karadima was suspended for life by the Vatican over the allegations of child molestation, and Barros was one of three bishops whose resignations Francis accepted on Monday.
Barros 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.
Several members of the church hierarchy, including former bishop Juan Barros, are accused by victims of ignoring and covering up years of child abuse by Chilean paedophile priest Fernando Karadima during the 1980s and 1990s. They have already compiled a report that says the Chilean Church covered up abuse cases and destroyed evidence.
The 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.