Blatter was asked at the Oxford University Union on Friday for his opinion on Real Madrid and Portugal forward Ronaldo and Barcelona's World Player of the Year Lionel Messi.
Ronaldo was the last player to land the World Player award in 2008 before Argentine Messi won four in a row.
Blatter said they were both exceptional players but added that, unlike Messi, Ronaldo resembled "a commander on the field of play". He then rose from his chair and strutted on the stage in military fashion in apparent imitation of the Portuguese.
"One (Ronaldo) has more expenses for the hairdresser than the other but that doesn't matter," he added to widespread laughter. "I cannot say who is the best, there will again be a contest this year - I like both of them but I prefer Messi."
FPF president Fernando Gomes described Blatter's comments as "unfit and inappropriate".
"It was with surprise I watched and analysed the words of Sepp Blatter about the captain of our national team," Gomes said in a statement.
"I think the comments ... show a clear lack of respect both towards Ronaldo and Portugal, a country that lives its football intensely."
Gomes also said it was "inappropriate" that, on the day Ronaldo was nominated as a candidate for FIFA's Player of the Year award, the head of soccer's governing body showed a preference for Messi.
"We sent FIFA a letter asking for the president to tell us what are the real intentions of his words since we do not understand how he could make such comments," added Gomes.
Earlier, coach Carlo Ancelotti explained that Real president Florentino Perez had written to FIFA to ask them to clarify remarks he said showed "a lack of respect to a very serious and very professional player".
"I am completely in agreement with my president," the Italian told a news conference ahead of Wednesday's La Liga home game with Sevilla.
"I haven't spoken to Cristiano Ronaldo about it. He trained very well today, as always. He is showing every day he is a great player and that he respects everyone."
(Reporting by Iain Rogers in Madrid, Daniel Alvarenga in Lisbon; editing by Tony Jimenez)
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