A group of teenagers hurled insults at the AC Milan star as he did laps of the pitch at Coverciano.
Balotelli shrugged off the incident but did tell team-mates it was “unbelievable” and that this kind of incident would only happen in “Rome or Florence”.
The president of the FIGC Giancarlo Abete said: “It was unacceptable behaviour on the part of the individuals who, by their actions, have demonstrated a lack of class.
“But we have to put it into context. The important thing is that there were only a few people involved.”
Italy coach Cesare Prandelli added: “I only heard nice chants. If there is more than one who makes headlines there is nothing I can do about that.”
Dario Nardella, the governing mayor of Florence, was disappointed the incident had occurred on his patch.
He said: “They were unacceptable insults hurled at Balotelli. It is even more serious as it came from a young fan.
“Florence is against racism and promotes respect, education and culture.”
Balotelli’s Italy team-mate Ciro Immobile expressed his disgust at what had happened but praised the way the former Manchester City striker handled himself.
He told a press conference: “In 2014, we shouldn't have to deal with racism.
"We have to improve as a nation. Fortunately, Mario was very calm.
"We will try to make appeals so these episodes do not happen again.
"I'm not ashamed of being Italian, but I do get upset by this type of behaviour."
Italy face the Republic of Ireland in London on May 31 in a friendly before heading to Brazil. They were drawn in Group D with England, Uruguay and Costa Rica.