Michael Garcia, FIFA's ethics investigator, who conducted an 18-month inquiry into allegations of corruption surrounding the bidding processes for the 2018 and 2022 World Cups, has questioned the findings released today.
The 42-page report cleared both Russia and Qatar, who will host the 2018 and 2022 tournaments respectively, of wrongdoing.
But Garcia, a United States attorney, who filed a 350-word report on the investigation in September, says today's report "contains numerous materially incomplete and erroneous representations of the facts and conclusions".
"I intend to appeal this decision to the FIFA Appeal Committee," he added.
The statement, issued less than four hours after the report was published, reopens the debate about the validity of the bidding process for both the 2018 and 2022 competitions.
In response, a FIFA spokesman said: "For the time-being, FIFA has not been officially notified of this statement and is therefore not in a position to further comment on this matter at this stage.
"We will follow-up in due time."
British MP Damian Collins, who has campaigned for FIFA reform and in 2011 used Parliamentary privilege to make allegations that bribes helped secure Qatar the 2022 tournament, believes the FIFA Ethics Committee's report is flawed.
"It is a whitewash," said Collins.
"FIFA has investigated itself and not surprisingly found itself not guilty.
"The truth remains that the serious allegations of bribery, of payments from bidding countries to senior FIFA executives, that's never properly been investigated by FIFA.
"The truth is they just don't know and yet they are prepared to say they are not guilty, there's no problem here."
Hans-Joachim Eckert, chairman of the Adjudicatory Chamber of the FIFA Ethics Committee, who wrote the report, based it on the work of Garcia.
"I cannot comment, I don't know why he has said this, I need to speak to him," Eckert told the BBC.
Speaking to the Press Association Sport, Jim Boyce, Britain's FIFA vice-president, said: "In view of the fact Michael Garcia has now stated he is not happy with the findings and is to appeal, I await with interest to see what further disclosures will be made.
"I have always said as much of the report as it is legally possible to publish should be made public."
The report criticised England's bid for the 2018 tournament, with the Football Association's relationship with former FIFA vice-president Jack Warner highlighted.
"It is a politically-motivated whitewash and I am not sure how we can have confidence in the outcome of this report," former England 2018 chief operating officer, Simon Johnson, told Press Association Sport.
"The headlines today end up being about the England bid when it should be about how it has exonerated Qatar, which has overseen the deaths of hundreds of migrant workers and which has been described by the US Government as funding terrorist organisations.
"In relation to England's bid, I was satisfied at all times that we complied with the rules of the ethics code.
"We also gave full and transparent disclosure to the investigation which many others did not do.
"All these things are being said about England when the investigation was set up around the terrible allegations about corruption involving Qatar."
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November 2014: FIFA report into alleged corruption clears Qatar to host 2022 World Cup
November 2014: Qatar to be cleared of corruption over 2022 FIFA World Cup bid
October 2014: Report into 2018 and 2022 World Cup bidding processes won't be published in full, says FIFA's Ethics judge
October 2014: FIFA chief ethics investigator Garcia reiterates call for transparency
October 2014: Former FIFA watchdog member calls for Blatter to resign to restore "credibility"