Benitez has had to contend with quotas in European football for several years, but now he fears for the overall quality of the English game. The new regulations mean there will have to be eight home-grown players in every 25-man league squad from next season.
"Maybe it has been brought in too soon," said Benitez.
"In the Champions League we had two or three years to increase the numbers of home-grown players.
"The problem in England is that there is a big gap between the academies and the first team, the reserve league is not filling this gap.
"It may now be difficult to maintain quality, but we will continue to do our best. The number of players is not the point, the quality is the point. But if they have decided this maybe they have been thinking about this rule for a long time."
Arsenal manager Arsene Wenger rejected the Premier League's new rules on home-grown players as "artificial".
The Gunners have a strong academy development programme, which takes in the cream of talent from around the globe, bringing though the likes of current captain Cesc Fabregas and full-back Gael Clichy.
Speaking in Belgium ahead of Wednesday night's Champions League Group H opener against Standard Liege, Wenger declared: "I am not in favour of it, and I said that many times.
"I feel that when you want to see the best players in the best league in the world, you have to be open. To accept competition - and we live for competition - it is not to accept artificial rules and that is why I am against it."