FIFA selected their eight seeds based on the world rankings from November with hosts Brazil joined by Spain, Germany, Argentina, Colombia, Portugal, Uruguay and Switzerland with Italy just missing out.
Since the seeds were announced, Italy have leapfrogged Switzerland into seventh position, which would have earned them a spot in Pot A of the draw.
Prandelli, who qualified Italy for Brazil 2014 with two rounds of qualifying to spare and reached the Euro 2012 final, believes his team deserved better.
"I'd say FIFA should reconsider the draw issue in future, especially as I've been told we are now seventh in the world ranking again," Italy's coach told RAI Sport.
"That makes it a bizarre situation."
In the rehearsal draw, Italy were grouped with Brazil, France and Australia and Prandelli revealed he and French coach Didier Deschamps were unimpressed on their flight to Bahia, where the actual draw will be held on Friday.
"The virtual draw yesterday was a little game I did not enjoy," Prandelli said.
"The coach of France, Deschamps, was sitting next to me on the flight and he didn't enjoy it either."
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