FIFA president Sepp Blatter was re-elected for another four years last week but was the only candidate after Asian football chief Mohamed Bin Hammam pulled out after being investigated by FIFA into alleged corruption during his campaign.
The Football Association, which had already said it would abstain in the vote, wanted the election postponed and Cameron has now made his views clear having been involved in England's failed 2018 World Cup bid
"Personally, I have seen football governance at an international level and I wasn't that impressed by what I saw," he told parliament.
"FIFA's reputation is now at an all-time low, and obviously the election with just one candidate was something of a farce but it has to become more transparent and more accountable. They've got to prove that they are actually capable of doing the job that they are meant to.
"But ultimately change has got to come from within football and I am sure that the FA will want to play a very major role in helping to bring that about."
The bids to host the 2018 and 2022 World Cups were mired by allegations of corruption with two members of FIFA's Executive Committee suspended after accusations they wanted money for votes.
Russia won the 2018 hosting rights and the 2022 tournament went to Qatar, which has denied newspapers allegations they "bought" the World Cup.
Blatter has said that the next World Cup hosts should be chosen by all 208 member associations of FIFA and not just the 24-man executive committee.
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