Allegri employed the formation for their Champions League defeat at Malaga.
“Is it the sign of a new era? That seems a bit much, we are simply playing with three centre-backs,” Galliani told Sky Sport Italia.
“In 26 years of President Silvio Berlusconi’s reign we have used this system with Alberto Zaccheroni. Many top clubs are using a three-man defence at the moment.
“We knew that it would be a new Milan this season. Last year we finished second in Serie A and could so easily have won, but now it will take a little patience.
“Everyone wanted a younger Milan, now they are accusing us of ruining the squad. I hope the fans have patience with us too.
“Now we have to get back our confidence. It’s true our squad is inferior to previous years, but remains first class.
“We cannot be considered a side worthy of the bottom spots.”