The Frenchman is particularly concerned with players unable to play against their parent club, claiming the system is flawed - with the Gunners set to face a Toffees side at Goodison Park consisting of Manchester City's Gareth Barry and Chelsea's Romelu Lukaku.
Wenger said the loan should be a total one - that is, the player is eligible to play against his parent club - to protect the integrity of the league.
"I believe that if you want to continue the system we have to make them available against the teams that loaned them out - or the system is not defensible," he said.
"It is just a protection of the clubs who loan the players out to hurt their opponents, when they have no risk at all.
"For a while you could decide when you loaned a player out whether he could play against you or not and I always decided 'yes, he can play against us'.
"The system is the same for Chelsea, Arsenal and everybody else but the only question is 'is the system right or not?' It is open for debate.
"It is true Everton have done a quality job on that front because they have got Barry, Lukaku, Gerard Deulofeu from Barcelona.
"Lukaku and Barry, yes they have been influential."
Wenger said, however, he does not believe title challengers loan deliberately to rivals in order to derail sides their players will invariably have to play against.
"I don't think so – I think it is just a chance to loan the player somewhere at the top level and see how good he is, which we try to do as well, but it raises questions," he added.
"This is not something against Chelsea or Man City, it's just that the whole system has to be considered."
Wenger also weighed in on the current saga surrounding Chelsea and 'feeder club' Vitesse Arnhem in the Eredivisie, with the Dutch FA investigating claims the Blues ordered them to lose games.
The Arsenal boss said there is a query on whether Vitesse are playing at 100 per cent, with claims Chelsea would prefer they did not reach the Champions League so as to not cup-tie any loanee players.
"I think the best thing would be that players are only loaned to the lower divisions and abroad – and even abroad, I am not completely convinced that it is right," Wenger said.
"For example, I read in a paper that in Holland they complain that Vitesse Arnhem doesn't want to win the championship – so that is the kind of question you get in the modern game.
"We are interested in feeder clubs as well but it is true it raises questions."