The rules introduced by the Premier League, adapted from UEFA's Champions League squad rules, state that clubs have to register a squad of no more than 25 players, which must include at least eight "home-grown" players, at the end of each transfer window.
"I believe it's a disastrous decision for football and for the players and I am quite amazed that the (players') union accepted that," the Frenchman said. "I believe it's also a very bad decision for the clubs."
The idea is designed to increase the number of young "home-grown" players in England's top division.
Ironically, Arsenal skipper Cesc Fabregas, who has just won the World Cup with Spain, would qualify as a "home-grown" player because he joined Arsenal at 16 and is now 23. The new rules will not impact unduly on Arsenal's senior squad, as Wenger has at least eight players who qualify for the home grown rule.
"I am not a big fan of it, because it means many players will be without clubs - that's the first mathematical consequence of it," he told a news conference ahead of this weekend's pre-season Emirates Cup tournament.
"Secondly, it puts the clubs in a weak position most of the time in the transfer market because when you already have 25 players, when you buy a player, you have 26 and you have to get rid of one.
"So you have to integrate when you buy a player, how much it costs to get rid of a player."
Asked if it was better to have the new system rather than the richer clubs "stockpiling" players, Wenger replied: "It's always about negative thinking. The big clubs have 25 top players anyway, you will not stop that by this kind of decision.
"There are only two solutions. If the big clubs have already employed a player, he has to go to a smaller club.
"The smaller club pays more than its potential, or the bigger club pays part of the salary, so in both cases it's not satisfying."
