The Spanish champions were sanctioned on Wednesday by FIFA's disciplinary committee for breaking regulations in the cases of 10 under-18 players, and have been punished with a transfer embargo covering two windows and fined 450,000 Swiss francs (£305,000).
Barca subsequently announced they would be appealing against the ruling to FIFA and, if necessary, would then take their fight to the Court of Arbitration for Sport (CAS).
Wenger believes the whole system needs to be examined for the long-term good of the global game.
He said: "Certainly they have not respected the rules.
"The rule is quite simple, you cannot move the players before the age of 16 unless their parents move for professional reasons, so that of course creates a bit of a debate - do the parents move for professional reasons or not?
"In this case, FIFA has judged the parents moved for football reasons and that is why they were banned because they have not respected the rules."
Wenger added: "I think the rules need to be changed, because there is more competition now to get the young players, and you will always be in a debate as to why did the parents move?
"There is more money in the game, so the parents will be tempted to give their young boys a chance to have a great career.
"What is not right is that the children move under the age of 16 without their parents. That is absolutely not right.
"Do they have to change the rules so you allow children to move with their parents if the club takes care of the parents? Maybe we have to go that way because it happens."
Arsenal themselves were once criticised by Barcelona for taking on Cesc Fabregas as a youngster after the player had initially been at their academy.
Wenger added: "At the time they were critical of us, you look at their players who came out from their youth academy are people like (Andres) Iniesta. He came (to Barcelona) at a very young age from the north of Spain, so they have always scouted people all over Spain."