Webb has 28 caps and is therefore set to miss out on test rugby after agreeing to join the French club next season.
"I had a good conversation with Rhys," Gatland told reporters on Monday.
"He can still get out of his Toulon contract. He has just signed a letter of agreement. He has not signed a full contact with Toulon.
"He has had a lot of injuries, he is 28, getting to 60 caps might take three years and he might not get that opportunity (to move) again.
"You have to feel for him. From my point of view, we potentially won't be able to pick a world class player. That's disappointing."
Webb has been a mainstay in Gatland's squad when fit and said that he was still hopeful of a place in the squad for the November internationals against Australia, New Zealand, South Africa and Georgia.
"I have given 10 years' service to the Ospreys and Welsh rugby and have picked up injuries along the way," Webb told Wales Online on Monday. "I would have hoped that would have been taken into consideration.
"I still very much want to play for Wales this season and hope I can gain selection for the autumn international squad."
(Reporting by Aditi Prakash in Bengaluru, editing by Nick Mulvenney)
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