Greg Dyke made his comments after the man who investigated claims of wrongdoing said the report was “erroneous”.
Mr Dyke said: “It has undermined the whole process.” He said it now looked “pretty ugly for Fifa”.
The report cleared Russia and Qatar of corruption allegations but criticised the FA for flouting bid rules. The 42-page document was put together by German judge Hans-Joachim Eckert was published yesterday.
Less than four hours later, American lawyer Michael Garcia, who spent two years investigating claims of corruption, issued a statement questioning the report.
He said he would appeal against the decision to close the probe into how Russia and Qatar won World Cup hosting rights.
He would do so because the decision was based on “materially incomplete and erroneous” information.
In what appears to be an open act of conflict within Fifa, Mr Garcia criticised the clearing of the 2018 and 2022 hosts. Mr Eckert’s findings were based on Mr Garcia’s investigation.
The dispute between Mr Garcia and Mr Eckert further fuelled the turmoil surrounding Fifa’s decision to give the next two World Cups to Russia and Qatar.
In a statement, Mr Garcia said: “Today’s decision by (Eckert) contains numerous materially incomplete and erroneous representations of the facts and conclusions detailed in the Investigatory Chamber’s report. I intend to appeal this decision to the Fifa Appeal Committee.”
Mr Garcia had called for key details of his 430 pages of investigation to be published, provoking clashes with Fifa President Sepp Blatter.
Mr Eckert found that any wrongdoing found in Mr Garcia’s investigation did not affect the integrity of the December 2010 votes by Fifa’s executive committee.
Mr Eckert formally ended the probe almost four years after the vote by the governing body’s scandal-tainted executive committee. No proof was found of bribes or voting pacts in a probe hampered by a lack of access to evidence and uncooperative witnesses.
“The evaluation of the 2018/2022 Fifa World Cups bidding process is closed for the Fifa Ethics Committee,” the German judge wrote in a statement released by Fifa.
Mr Eckert’s report reserved his harshest condemnation for England’s failed bid for the 2018 tournament. It criticised England for wooing disgraced former Fifa vice president Jack Warner and “damaging the image of Fifa and the bidding
The 2022 World Cup will finally, it seems, be played in Qatar – although exactly when is still unclear as Fifa seeks an alternative to the desert heat in June and July.
“Fifa welcomes the fact that a degree of closure has been reached,” the governing body said in a statement. “As such, Fifa looks forward to continuing the preparations for Russia 2018 and Qatar 2022, which are already well under way.”
The Qatari organising committee said it would study the report before commenting. Despite finding wrongdoing among the 11 bidding nations, Mr Eckert said the integrity of the December 2010 votes was not affected.