Fifa selected its eight seeds based on the world ranking, with hosts Brazil joined by Spain, Germany, Argentina, Colombia, Portugal, Uruguay and Switzerland, while Italy were one of the top nations that just missed out.
Since the seeds were announced, the Azzurri have leapfrogged Switzerland into seventh position, which would have earned them a spot in Pot 1 of the draw, leaving Prandelli incensed.
"I'd say Fifa should reconsider the draw issue in future," Italy's coach told Gazzetta dello Sport.
"Everybody can see something isn't right with the current system. Are we looking at the Fifa Ranking? Alright, we're seventh again now and have been among the top seven countries for about two-and-a-half years.
"Yet we're only looking at October. That's a bit ridiculous. That makes it a bizarre situation."
Italy are one of nine countries in Pot 4 for Friday's draw in Costa do Sauipe.
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