The Milan striker, 23, was subjected to racist chants at the training base in Florence last Wednesday, with police needing to intervene.
While eager to move on from the incident, Prandelli – who signed a two-year contract extension with Italy on Monday – hit out at the person responsible.
"I am sorry to go over this topic again. However, I would like to stress that 99 people out of 100 were applauding and supporting our players," Prandelli told a news conference.
"Then one idiot popped by, but an idiot does not make the difference.
"The day after, Mario had the solidarity of Florence, especially from lots of children who cheered him up and brought by some cakes for him.
"The problem is that things done by one idiot should not be newsworthy."
Prandelli was full of praise for Balotelli's fellow striker Giuseppe Rossi, who has overcome an injury-riddled campaign to be close to a FIFA World Cup place.
The 27-year-old Fiorentina man was praised for his hard work and dedication and Prandelli said the United States-born 27-year-old was an example for the rest of his squad.
"When I think about Rossi, I see a guy making great sacrifices and dreaming with open eyes," Prandelli said.
"That's a message that should make all the players of this squad reflect."
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