Criscito admitted to being stunned by being left out of Italy's 30-man squad by Prandelli earlier this month.
However, Prandelli responded to the controversy over the decision by joking that "he had not left behind Antonio Cabrini or Paolo Maldini".
But the 56-year-old has now expressed regret at his remarks, conceding that they were "out of place".
"I didn't cut anyone who had just played a Champions League final. Having said that, I want to apologise to Criscito for the joke I made about Cabrini and Maldini," Prandelli said.
"It was out of place and I didn't want to get into the technical merits of the exclusion."
Italy's squad will need to be reduced to 23 players by June 2, and Prandelli, speaking at the first day of training ahead of the tournament, wants every player to compete as much as possible to prove their worth.
"I hope that I have doubts to the last minute, as that will mean all 30 arrived with enthusiasm and hunger," he added.
"I hope that the media get involved in this campaign too. We represent all of Italy.
"They must all be aware that even in a few minutes they can still make their mark on the field. We must all put aside the 'I' and remember to be a team."
