FIFA ethics investigator Michael Garcia has resigned, a day after his appeal over a decision by ethics judge Hans-Joachim Eckert was ruled inadmissible.
World football's governing body was plunged into chaos last month when Eckert said there were no grounds to reopen the controversial bidding process which led to Russia being given the 2018 finals and Qatar the 2022 tournament.
FIFA and Qatar World Cup organisers have been fending off allegations of corruption ever since the Gulf state was awarded the 2022 tournament.
In his resignation statement Garcia says: "No independent governance committee, investigator, or arbitration panel can change the culture of an organisation."
The American lawyer cited a "lack of leadership" at the top of football's world governing body.
Garcia said he lost confidence in the independence of judge Hans-Joachim Eckert, an ethics committee colleague.
UEFA president Michel Platini says: "We wanted all transparency but this is a new failure for FIFA."
FIFA president Sepp Blatter says he is surprised by Garcia's decision, but the work of the ethics committee will nonetheless continue.
The association said in a statement that an acting chairman of the committee would be appointed, pending the election of a successor to Garcia.
Russia won the right to host the 2018 World Cup, while Qatar was awarded the 2022 tournament. FIFA cleared both of corruption despite a series of allegations.
Qatar whistleblower Phaedra Al Majid claims Garcia's resignation is "one more, emphatic exposure of FIFA's self-protecting corruption."
She adds: "Its rules are a farce. Not even an extensive, purportedly independent, two-year investigation and report could affect its culture. Why would anyone believe or trust anything it says?"