Read more: More charges set to be brought in Fifa probe
The Swiss attorney general has brought charges of criminal "mismanagement" and "misappropriation" against Blatter, who had previously avoided any allegations specifically against his person in the corruption scandal engulfing Fifa.
Blatter was "interrogated" by attorney general representatives today, as Fifa cancelled a planned press conference at the last moment.
The charges centre around a payment made to Uefa president - and potential Blatter successor - Michel Platini and an "unfavourable" contract signed with the Carribean Football Union while disgraced former president Jack Warner was in charge.
Police have seized data from the divisive president's office and contacted Platini for further information.
Swiss authorities had been investigating claims of corruption in the bidding process for the Russia and Qatar World Cups in 2018 and 2022.
In a statement, the office of the attorney general explained that the 2005 contract signed with the Carribean Football Union may have seen Blatter violate his duties and act against his interest as Fifa boss.
A "disloyal" payment to Platini in 2011 for work performed between 1999 and 2002 - while Platini was one the Fifa executive committee - may have also "acted against the interest of Fifa".
In response, Fifa said it was continuing to cooperate with the investigation and has "complied with all requests for documents, data and other information".