FIFA secretary general Jerome Valcke put on leave and relieved of duties with immediate effect.
A FIFA press release said it had "been made aware of a series of allegations involving the secretary general and has requested a formal investigation by the FIFA Ethics Committee."
Valcke was earlier accused of being implicated in a scheme to sell Football World Cup tickets above face value for a share in profits.
The allegations, denied by Valcke, have been made by a consultant at a company that struck a deal with FIFA to sell tickets for the 2014 World Cup but the contract was cancelled.
The 54-year-old Frenchman, who has been FIFA president Sepp Blatter's right-hand man since 2007, is alleged to be the beneficiary of an agreement to sell the tickets at inflated prices.
FIFA have been embroiled in a major corruption scandal since the arrest of seven of its officials on May 27 attending a FIFA congress in Zurich to elect a new president.
They are among 14 people charged by US authorities over more than $US150 million in bribes given for television and marketing deals.
Despite the arrests in May the election went ahead with Blatter winning a fifth mandate although he then announced he would be standing down with a new election scheduled for February.
Valcke was not implicated in the FIFA corruption scandal although he has been a steadfast supporter of Blatter.