Several clubs have been punished this season for anti-Naples chanting by fans, an offence officially termed "territorial discrimination", even at matches at which Napoli have not been playing.
The sanctions have been implemented as part of new guidelines which were originally intended to crack down on racial discrimination.
"The problem is not the rule, which is something we have received from UEFA, but the way it is implemented which is very limited," Beretta told Gazzetta dello Sport.
"We are punishing the minority of uncivilised people the hard way, but we can't continue to punish the majority of respectable fans as well.
"I'm sure they share our fight against racism which, I repeat, is something we will not back down from.
"The current system is proving to be something of a boomerang."
Italian fans have long exchanged regional insults and some of the recent chanting has been interpreted as an act of defiance against the new rules.
In October, Inter Milan fans started a campaign inciting all supporters to break rules simultaneously with the intention of having an entire weekend where all the matches were played behind closed doors.
The most recent case involved AS Roma who were ordered to close both the Curva Nord and Curva Sud sections at the Stadio Olimpico following recent chanting.
They served the first match of the ban at home to Sampdoria on Sunday, when fans in the section adjacent to the Curva Sud, known as the Distinti, also took part in anti-Naples chanting.
That section of the stadium has also been ordered closed for Roma's next home game.
(Reporting by Brian Homewood; Editing by Rex Gowar)
