The governing body's president told Swiss TV station RTS that FIFA had made "a mistake" in awarding the Arab state the right to stage the tournament.
However, FIFA have stressed that the 78-year-old's remarks were misinterpreted, stating that the Swiss was instead referring to the decision to organise the 2022 tournament in the northern hemisphere summer.
A FIFA statement read: "The comment by the FIFA President concerning the organisation of the 2022 FIFA World Cup in Qatar to Swiss TV station RTS is in line with previous comments on this matter.
"As explained in his answer to the journalist, the President reiterated that the decision to organise the World Cup in summer was an "error" based on the technical assessment report of the bid, which had highlighted the extremely hot temperatures in summer in Qatar.
"At no stage he questioned Qatar as hosts of the 2022 FIFA World Cup."
The decision to award the 2022 World Cup to Qatar has been marred by allegations of bribery and concerns over the extreme heat in the Arab state during the months of June and July, when the tournament traditionally takes place.
Fears over the dangerous temperatures in Qatar in that time of year have led to calls for the competition to be moved to a different date, with switches to November or January mentioned as potential solutions.
