The Welsh Rugby Union last week outlined plans to change the selection criteria from the current wildcard system to one where players who ply their trade outside of Wales will need to have at least 60 international caps to be eligible.
The new law will come in to effect from next season and Ospreys scrum-half Webb is set to be the biggest casualty having already agreed to join French side Toulon from the start of the 2018/19 campaign.
Webb currently has 28 caps to his name and therefore falls well short of the new WRU requirements, meaning he will likely miss out on selection for the 2019 World Cup.
The 28-year-old, who has been included in Wales' autumn internationals squad, has branded the situation a joke but Gatland insists the new system, similar to the one used by South Africa, is better.
The Wales head coach has not been happy at the reaction to the change, though, believing it is unfair he bears the brunt of the criticism received over the Webb saga.
"There was a lot of criticism of myself over this, and I felt that was unfair," said Gatland.
"The policy we have is better [than the previous wildcard-based one] but I feel for Rhys in that he is not going to be available for the World Cup. We had a good chat about that when we met up last Saturday."
Regarding the new system. Gatland added: "I was consulted on it, I wasn't involved in the process. I got pushed out there from a media perspective on the Monday, and it was almost like it was my policy.
"We haven't heard one word from the regions at the moment about their involvement in that, and I would like to hear from them."