Rossoneri midfielder Kevin-Prince Boateng led his team-mates off the pitch during a friendly match at Pro Patria last week after being subjected to racist chanting from a section of the home fans.
Leading authority figures, campaigners and current professional footballers were quick to lend their support to the former Portsmouth and Tottenham player, who insisted he would walk off again in any competitive match under similar circumstances.
Blatter said there should be "zero tolerance" for racism in the game but did not feel the solution was for players to "run away" from racist abuse.
Berlusconi rejected the FIFA president's position, telling radio station RTL: "I am of the opposite view.
"In fact, I thanked and congratulated my players for their decision to leave the field during the friendly in Busto Arsizio.
"This is an uncivilised problem that needs to be stopped, people should not allow these things to happen.
"Teams out on the pitch should set an example of civility and the educational role of football should not be underestimated.
"It's not only about the behaviour of players in the game, but of the public, and everyone needs to avoid giving Italy a negative image."
Piara Powar, the executive director of anti-racist campaign group Football Against Racism in Europe (FARE), told The Guardian: "We disagree entirely with the idea that Kevin-Prince Boateng ran away from the Milan match in which he was subjected to racial abuse. It's a nonsensical suggestion.
"What does Sepp Blatter know about what it is to be abused or excluded because you are an ethnic minority, and what might be the right or wrong way to respond?
"The point is that the hard-won processes put in place to deal with issues of discriminatory abuse, that apply from referees all the way up to international disciplinary commissions, are not being implemented.
"There seem to be so many statements being made off the cuff by football administrators on important issues of policy that are ill-thought out. The message going out is one of indifference by governing bodies at all levels."
Speaking at a conference in the Middle East, Blatter had told United Arab Emirates newspaper The National, he said: "Walk off? No. I don't think that is the solution.
"But the Italian federation has yet to provide FIFA with the report detailing what exactly has happened.
"I don't think you can run away, because eventually you can run away if you lose a match. This issue is a very touchy subject, but I repeat there is zero tolerance of racism in the stadium; we have to go against that. The only solution is to be very harsh with the sanctions - and the sanctions must be a deduction of points or something similar."
Former Barcelona coach Pep Guardiola backed the decision by Boateng to walk off the field after being abused during a friendly, and his Milan team-mates for following him off the pitch.
Guardiola, speaking at the FIFA Ballon d'Or awards in Zurich, said it could deter racists in the future.
He told a news conference: "Maybe it was a good step to take. Maybe with Milan dealing with this situation in that way means that it won't happen again."
Both Cristiano Ronaldo and Andres Iniesta said Boateng had taken a "personal" decision which they understood.
Real Madrid star Ronaldo said: "Why this racism is still happening is incredible.
"I think it was a very personal decision by him - if he's very angry, if he's sad if he's feeling particularly sensitive then that's his decision. It depends on how you are feeling at that moment.
"We have to deal with these people in the stadium - perhaps they have a screw loose."
Iniesta, Barcelona's Spanish international midfielder, added: "The sad thing is that these things actually do happen. It is a very sad thing and a personal reaction by him."