Speaking at an event at Oxford University last week, Blatter said he preferred four-time World Player of the Year Lionel Messi to Ronaldo, who he claimed spends more money on his hairstyle than the Argentine.
Ronaldo has finished second to Messi in three of the last four years in the voting for the Ballon d'Or, although the Portuguese did win the award whilst still at Manchester United in 2008.
And both men were once again selected in the shortlist of 23 for this year's award which was released on Tuesday. "This video shows clearly the respect and consideration that FIFA has for me, for my club and my country," Ronaldo said on his official Facebook page.
"Much is explained now. I wish Mr. Blatter health and a long life, with the certainty that he will continue to witness, as he deserves, the successes of his favourite teams and players."
The comments also enraged Ronaldo's club and country as both Real Madrid and the Portuguese Football Federation (FPF) sent letters to FIFA to complain about Blatter's conduct.
However, in a reply to Madrid, published on the club's website, Blatter defended his comments and said he believes Ronaldo is on a par with Messi as a player.
"In response to a question about Lionel Messi and Cristiano Ronaldo, the moderator asked me to choose between one of the two and, in this moment having commented that Messi is the type of son all mothers would like to have, I ended up saying his name.
"However, I want to make it clear that for me Cristiano Ronaldo is at the same level as Messi and that they are both exceptional players, each one in their own way.
"It was never my intention to upset or show a lack of respect towards Real Madrid, one of their players or their fans." Madrid boss Carlo Ancelotti said the comments lacked respect for a player he described as a "great professional".
"It seems to me like a lack of respect," remarked the Italian. "I haven't spoken with Cristiano about it. Today he trained very well as he always does.
"He shows every day that he is a great player. He is serious, professional and respects everyone." And a statement on behalf of FPF president Fernando Gomes on the federation's website was even more damming of Blatter's behaviour.
"I can't, in any way, agree with the position expressed by the person who leads world football in his comments about the national team and about someone who is a symbol of Portuguese football," he said.
"Moreover, they seem unfit and inappropriate and clearly show a lack of respect for Cristiano Ronaldo and for Portugal.
"We learned today that Cristiano Ronaldo was one of the nominees for the Ballon d'Or, it does not seem appropriate or adequate that the president of FIFA makes comments saying which player he prefers between one or other."