Sepp Blatter admitted he was "surprised" to see Lionel Messi voted the World Cup's best player.
Messi picked up the Golden Ball award after Argentina's 1-0 defeat by Germany in the World Cup final.
The 27-year-old scored four goals in the tournament, but failed to add to his tally in the knockout phase and was unable to influence the game against Germany.
"I was a little bit surprised to see Messi coming up as the best player in the competition," the Fifa president told a press conference.
Argentine Diego Maradona earlier said his compatriot did not deserve to win the accolade, claiming the decision was influenced by "marketing" decisions.
Barcelona striker Lionel Messi has arrived at court to answer charges of tax evasion. The court will hear allegations that both Messi and his father Jorge withheld more than four million euros (£3.4m) by filing incomplete tax returns for the years 2006 to 2009.
His father Jorge Messi appeared in court an hour earlier. The World player of the Year and his father have both denied wrongdoing, and they have already made a 'corrective payment' to Spanish authorities of just over five million euros.
Lionel Messi and his father Jorge have been summoned to court in Spain as part of an investigation into tax fraud allegations.
A court in Gava, near Barcelona - where Messi plays his football - accepted a prosecutor's complaint that Messi and his father defrauded the Spanish tax office of €4m (£3.4m) and the pair are scheduled to appear on September 17th.
Barcelona football star Lionel Messi said he was "surprised" by allegations from Spanish tax authorities that he owes them more than €4m (£3.4m).
In a statement released to Spanish news agency EFE he said:
"We have just known through the media about the claim filed by the Spanish tax authorities. We are surprised about the news, because we have never committed any infringement.
"We have always fulfilled all our tax obligations, following the advice of our tax consultants who will take care to clarify this situation."
Barcelona football star Lionel Messi and his father have been accused by Spanish tax authorities of defrauding the state of more than €4m (£3.4m).
World Player of the Year Messi and his father Jorge allegedly filed fraudulent tax returns for the years 2006, 2007, 2008 and 2009, according to a spokesman for the prosecutor's office for tax crimes in Catalonia.
The Argentinian forward is on an estimated €16m (£13.5m) annual salary at Barcelona.
A solid gold replica of Lionel Messi's left foot was unveiled by a Japanese jeweller in Tokyo today.
The golden foot, made by the Tanaka Kikinzoku firm, is valued at around £3.5m.
Barcelona and Argentina star Messi, who has won FIFA's Ballon d'Or award for the last three years , said: "I'm honoured to have my foot recreated in pure gold."
Manchester City striker Sergio Aguero congratulated his Argentina team mate Lionel Messi on his record fourth Ballon D'Or victory:
QPR winger Shaun Wright-Phillips and former Barcelona player Gary Lineker also took to Twitter:
Barcelona's official Twitter feed has been waxing lyrical about the Argentine's achievement.