Wenger accepts his gamble to throw veteran centre-half Gallas back into action against Barcelona following eight weeks on the sidelines with a calf problem failed to come off after the defender was unable to complete the match.
"Now a club is not even any more in a situation when it can decide when it plays its players," said Wenger following Saturday afternoon's Premier League victory over Wolves.
"Clubs have the right to pay the players, but not when to play them.
"I don't disagree that I took a gamble on Gallas - but the player declares himself fit, the medical staff declared him fit, the rehabilitation centre declared him fit... but I still cannot play him because maybe France needs him in the summer in the World Cup - during which we pay him as well.
"You have to leave some freedom to the club to decide when they play their players."
Wenger has also seen his plans at Arsenal scuppered by injuries to key men while away on international duty.
The Frenchman said: "I want the players to do well for the national team as well, but the national teams have to accept as well that we lose the players.
"Like Robin van Persie, who went for what? To play in Italy in Bari for a friendly when the stadium is half empty - and we lose him for the whole season.
"We pay him the whole season. They decided to play him.
"So when we play at home against Barcelona in the quarter-final of the Champions League, we are still ostracised because we play a player who declares himself fit. That is a bit too much."