Real Madrid have written a letter to FIFA asking for President Sepp Blatter to explain comments he made about Cristiano Ronaldo during a talk at the Oxford Union recently.
Blatter was asked who he thought was the best player in the world between the pair, who have both been nominated for the 2013 Ballon d'Or.
The 77-year-old said he preferred Messi, and added that the Real Madrid star was the one more likely to spend his money at the 'hairdressers'.
He added that Messi has won the Ballon d'Or more times because he is a 'nice boy' who 'every mother would like to have at home'.
"They are both exceptional players but are totally different," he said. "Football is about the difference between stars. Lionel Messi is a good boy that every father, every mother would like to have at home.
"He is very quick, he is not exuberant, he plays well, he is a good boy. That is what makes him so popular, because he is this nice man and that is why he gets votes.
"The other one (Cristiano Ronaldo), he is something else, he is like a commander on the field of play.
"This is the other side of football and it is good to have such commanders on the field also. That gives life to football.
"One has more expenses for the hairdresser than the other, but that doesn't matter.
"I cannot say who is the best, there will be a contest this year and then January next year it will be announced. I like both of them, but I prefer Messi."
Real Madrid have seemingly taken exception to Blatter's comments regarding Ronaldo, and manager Carlo Ancelotti revealed today that the club have sought clarification over his remarks.
"The president has sent a letter to FIFA asking for a correction of what I consider disrespectful (comments) to a very professional player," the Italian said ahead of his side's clash against Sevilla.
"And I am in complete agreement with the president. I have not talked about this with Cristiano Ronaldo, who proves to be a great player. (He is) respectful to all parties, and should stay that way.
Cristiano Ronaldo has won the Ballon d'Or once before - back in 2008 while he was still with Manchester United.
Blatter's comments will do little to quell suggestions in Madrid that FIFA favour Messi as the best player in the world and Barcelona over Real.
While still in charge at the Bernabeu, Jose Mourinho failed to attend the Ballon d'Or gala, claiming that the award was fixed in Messi's favour.
He also boycotted the event because he felt the 'Coach of the Year' award was also rigged, claiming he had been told by some people that they had cast votes in his favour that weren't counted.