"We will not accept that situation to go on like that," Wenger told Arsenal TV Online.
"A player like (Abou) Diaby goes away and is injured and you cannot even get him back because they (France) decided to keep him. They knew from the first day on that he would never play for them but they didn't want to call another player up. So they decided to keep him and make everybody think he would play.
"The result? He comes back; the next day tries to have a little run and gets a setback and we have to deal with the consequences. It is disrespectful to the clubs, and it is not acceptable for the clubs. We pay the wages.
"For political reasons they keep the players in the squad and we have not a say, how can that work? Three days later you have to play a game and you have to win it. They don't care.
"Something has to change in there."
Wenger added: "In every other sport it is the club who decides if the player stays in the national team when he is injured. Only in our sport it is the federation who decides to keep the player if they want to keep the player. Why?
"That means they decide they are in a better situation to treat the player than you. Then they have to pay the player at the end of the month. Then they can decide, that would be logical. But you can do nothing because they have the rule in their favour."