The rule permits players to terminate their contracts after a "protected period", which for those under the age of 28 when they signed or renewed their deals is three years and for others, two years.
"The situation at the moment has become much more unstable with the Webster clause," he said. "Every new rule provokes a little bit more inflation and instability because the players can always move out earlier and quicker.
"For a club like ours, which is going for a youth-team policy, this rule is very detrimental. We educate them and then they could leave at some stage when they get mature. This rule is not good and we live in a world where it is also an incitement to inflation because you are always having to look at their contracts. Stability inside the club is a big problem because that problem is a huge inflation factor."
Wenger cited the case of Alexander Hleb, the 26-year-old midfielder he signed for £11.2m in July 2005, on a five-year contract. Wenger was upset to learn that Hleb was in Milan last month with an agent who brokers deals for Internazionale.
"Before, when you had a player under contract for five years, they were your player for five years; now, they can leave after three years [if they are] under the age of 28," said Wenger. "You are always confronted with potential instability. Players are admired all over the word, they are tapped up, agents get nervous and they see if they can do a deal."