In a statement, Fifa said its ethics committee had opened formal proceedings against Blatter and two other former officials, Jerome Valcke, who was secretary general, and Markus Kattner, former acting secretary general and director of finance and corporate services.
The body said it will look into potential violations of rules governing loyalty, conflicts of interest and bribery in the context of salaries and bonuses.
Under the Fifa Code of Ethics, the investigatory chamber shall examine all circumstances of the cases equally. For reasons linked to privacy rights and the presumption of innocence until proven guilty, the investigatory chamber will not publish further details at the present time
In June an internal Fifa report into corruption in the organisation found Blatter, Valcke and Kattner "enriched themselves" through pay rises and bonuses worth £55m over five years.
Kattner was sacked by Fifa in June after he was discovered making secret payments, while Blatter and Valcke have been banned from football for six and 12 years respectively on suspicion of criminal mismanagement - although both have denied any wrongdoing.
Earlier this year Fifa's offices were raided by Swiss authorities in connection with the scandal, with documents and electronic data seized.
In February Fifa elected Swiss-Italian lawyer Gianni Infantino to be Blatter's replacement - although Infantino has already cut a controversial figure after he was given the power to dismiss and appoint members of the independent ethics committee.