While comparing the Portuguese star to Lionel Messi, the Swiss executive said "one spends more time at the hairdresser's than the other."
During a debate at Oxford University over the respective merits of the Portugal international and Barcelona ace Lionel Messi, Blatter joked that "one spends more time at the hairdresser's than the other."
Ronaldo took offense, insinuating that the jibe underlined FIFA's bias against him and his club, but Blatter has now moved to calm the controversy by tweeting to the 28-year-old attacker.
"I apologise if you were upset by my light-hearted answer at private event on Friday," the Swiss wrote to Ronaldo's official Twitter account. "I never meant to offend you. I am an honorary 'socio' at Real Madrid and explained we've many talented players in world game, including you. Best wishes."
Blatter also addressed an open letter to Real Madrid president Florentino Perez to apologize for any offense caused.
He said: "Dear President, I have received your letter today, the contents of which surprised me. I want to clarify that for me Cristiano Ronaldo is at the same level as Messi and they are both outstanding players, each in their own way.
"I'm sorry that this situation produced in a university event hurt as much as it did, and I apologise for it. It was never my intention to embarrass or disrespect Real Madrid or one of their players or the fans, not only for being the founder of the FIFA club but also for being the club that I follow and admire from my youth."
Barcelona forward Messi has defeated Ronaldo to the last four FIFA Ballon d'Or awards.