Yoon was ousted on April 4 over his attempt to declare martial law late last year.
Prosecutors investigating an influence-peddling case involving religious figures were looking for documents and material that could indicate their association with the former president and his wife, Yonhap said, Reuters reported.
It was not clear if investigators had entered the premises, Yonhap said.
A spokesperson for the Seoul Southern District Prosecutors’ Office, which is handling the case, could not be reached for comment.
Following his December 14 impeachment by parliament, Yoon had resisted attempts by investigators to search the official presidential residence, citing reasons of security and protection of classified materials.
He moved to his private residence on April 11.