FIFA Secretary General, Jerome Valcke, has been put on leave and released from his duties until further notice.
A FIFA statement said it had “been made aware of a series of allegations involving the secretary general.”
Some allegations on Thursday implicated Valcke, 54, in a scheme to sell World Cup tickets for above face value.
The Frenchman, who has held his role at FIFA since 2007, said he denied the “fabricated, outrageous” allegations.
Football’s world governing body has been engulfed by claims of widespread corruption since May, when Swiss police raided a hotel in Zurich and arrested seven of its top executives.
United States officials have since indicted those seven and two other Fifa officials on bribery and racketeering charges.
President Sepp Blatter announced that he would stand down just days after winning re-election in June.
Valcke, who last month was considering standing to be the new president, is Blatter’s number two at the organisation but now faces a formal investigation by FIFA ethics committee.
Earlier on Thursday, Eugenio Figueredo, one of the seven officials arrested in May, had his extradition to the United States approved.
As well as the U.S. inquiry, a Swiss investigation is looking into the bidding process for the 2018 and 2022 World Cups.
FIFA has recently set up a taskforce to tackle corruption which aims to “restore the integrity and reputation” of the organisation.
