Authorities seized documents and electronic data from the football governing body's offices in Zurich as part of an ongoing probe into former president Sepp Blatter and his secretary general Jerome Valcke.
A statement from the office of the Swiss Attorney General read: "As part of the ongoing criminal investigations in the FIFA affair, the Office of the Attorney General of Switzerland (OAG) carried out a search of Fifa's headquarters on June 2, 2016 with the aim of confirming existing findings and obtaining further information.
"Documents and electronic data were seized and will now be examined to determine their relevance to the ongoing proceedings.
"The investigations still relate only to the persons named in earlier statements issued by the OAG and further persons unknown. As proceedings are ongoing, no further information can be given at present."
Fifa was not immediately available for comment.
Both Blatter and Valcke deny wrongdoing but have been banned by Fifa's ethics committee for eight - later reduced to six - and 12 years respectively.