The Milan forward has battled racism from supporters throughout his four seasons playing in the northern city, having spent three years at Inter prior to his Manchester City stint.
Balotelli has represented Italy 29 times but a selection of supporters in Florence on Wednesday made race-related chants towards the Palermo-born forward - who has Ghanaian heritage.
Italian Football Federation president Giancarlo Abete slammed the offending supporters.
"This is unacceptable behaviour," Abete said.
"This should not happen. The important thing is that this is only a minority and they have no regard for civil coexistence."
Balotelli's national team-mate Ciro Immobile said the fans reflected poorly on the country ahead of their World Cup challenge.
"It's unbelievable that in 2014 we still have this form of racism," Immobile said.
"It's not great for the nation. We represent Italy.
"It saddens me. To be hearing racist insults from people, whether you're yellow, black or white, is just unacceptable.
"Fortunately, Mario let it pass over him and he got on with his training. But we as players should do more to help stamp this out."
Immobile, who scored 22 goals for Torino to win the golden boot in the Serie A this season, said he was crushed by chants against his native Naples during the league campaign.
"When I hear that it saddens me, because I have a lot of pride in my city," he said.
"To hear fans shouting, 'Wash them with the lava from Mount Vesuvius' isn't very pleasant."
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