The Azzurri dominated Sunday's 0-0 draw with England in Kiev - the first game to go to extra time at the finals - before prevailing on penalties while the Germans defeated Greece 4-2 in regulation time on Friday.
"It's a problem that UEFA must consider for the next European Championship," he told a news conference on Monday.
"To play a semi with this small gap does not help the spectacle."
Daniele De Rossi and Ignazio Abate limped out during the energy-sapping 120 minutes against a burly England in Kiev, potentially leaving Prandelli without his most combative midfielder and only eligible right-back against the Germans.
Italy's other right-back Christian Maggio will be suspended after picking up a second tournament booking while centre-half Giorgio Chiellini and midfielder Thiago Motta have had minor niggles.
Prandelli fears Germany's fit and young side could be an insurmountable object given their quality on the ball and extra rest, even if they have never beaten Italy before at a major championship and lost the 2006 World Cup semi to their rivals.
"We meet an athletically strong team. We have to play the game on the small weaknesses that they might have. It's a difficult game where right until the last minute the result will probably be in the balance," he said.
"When we know who is fit, we'll see who we can play on Thursday. We know we can have another good game. We've got to read the game but paradoxically we've got to take some risks."
The soft-spoken but thoughtful coach was given a round of applause by Italian reporters on his return to Italy's 'Casa Azzurri' after surpassing expectations in reaching the last four.
His attempts to play a more expansive game than some Italy coaches of the past has also found favour with pundits and fans and he is not about to compromise his principles now, even in a semi-final against the might of Germany.
"We can do something more, play football even better. We have the responsibility to try it," he said.
"The new generation want to watch this type of football.
"We have to put more ideas on the pitch."
