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He made his comments after the man who investigated claims of wrongdoing said the report was "erroneous".
"It's a bit of a joke, the whole process," Dyke told BBC Sport, adding that it looked "pretty ugly for Fifa".
The report cleared Russia and Qatar of corruption allegations but criticised the FA for flouting bid rules.
Later on Thursday, on BBC's Newsnight, Dyke added that he could not "take the report seriously".
He said: "The whole of the way football operates at that sort of level is suspect and has been for many years. I don't think Fifa is a straight organisation and hasn't been for many years."
The 42-page document, published at 09:00 GMT on Thursday was put together by German judge Hans-Joachim Eckert. He based his findings on the work of American lawyer Michael Garcia.
But less than four hours later Garcia, who spent two years investigating claims of corruption for world governing body Fifa, issued a statement questioning the report.
He said Eckert's findings contained "numerous materially incomplete and erroneous representations".
Garcia said he intended to appeal to Fifa.
Fifa said it had yet to be notified by Garcia of his intention to appeal.
The FA was accused of trying to "curry favour" with former Fifa vice-president Jack Warner, who quit in 2011 amid bribery allegations.
The report said England's bid team tried to win the support of Warner, who is from Trinidad and Tobago, by:
Dyke said the FA had "nothing to hide".
"Within that report, most of the criticism is of people who co-operated the most fully," he said.
"If you actually didn't co-operate, you don't get criticised, which seems very weird to me. The FA, I don't think on this, has got anything to hide.
"Everything that was done was cleared with the Fifa executive beforehand and was told to the Garcia report by the English FA."
Dyke also called for Garcia's report, which runs to hundreds of pages, to be published in full.
Lord Triesman, chairman of the FA at the time voting for the 2018 and 2022 World Cups took place, said he also wanted to see the complete document after being criticised for failing to co-operate with the investigation.
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"I'm never satisfied by seeing summaries by somebody else," Triesman told BBC Sport. "In this day and age, people are entitled to see the original."
British MP Damien Collins described Eckert's report as "a whitewash" before Garcia's statement was issued.
Fellow MP Clive Efford, Labour's Shadow Minister for Sport, added: "Fifa has no choice but to publish Michael Garcia's report in full if it expects anyone to believe their claims that there has been no cover-up over allegations of corruption in the World Cup bidding process."
Fifa's inquiry looked at the conduct of the nine teams bidding to win the right to stage the 2018 or 2022 World Cups.
It was initiated after a number of corruption allegations were made once voting had taken place in 2010.
Russia won the right to host the 2018 tournament, beating England and joint bids from the Netherlands/Belgium and Spain/Portugal.
England collected just two votes after expressing high hopes of winning.
To much surprise, Qatar was awarded the 2022 event, edging out Australia, Japan, South Korea and the United States.
Qatar was subsequently accused of paying Fifa officials £3m to secure backing for its bid.
The report cleared the Gulf state of corruption, although it noted that there were "certain indications of potentially problematic conduct of specific individuals".
Hassan Al Thawadi, general secretary of the Qatar 2022 organising committee, told BBC Sport: "We've been transparent when it comes to the process of bidding for the 2022 World Cup.
"We've always been confident about the integrity of our bid. Today's report was confirmation of that."
The report noted that the Russian bid team made "only a limited amount of documents available for review".
According to the report, the Russian team hired computers that were subsequently destroyed, denying the inquiry access to email accounts.
"We were always confident that there could be nothing which would come out from this investigation," said Alexey Sorokin, the head of Russia's 2018 World Cup organising committee.
Fifa's report into World Cup corruption is now pointless and a joke, according to English Football Association chairman Greg Dyke.