Inaki declared staging the competition in Saudi Arabia "sucks" as it takes him away from his family, with his wife due to give birth.
In response, Valverde said: "Regardless of whether we like the format or not, I'm not sure his words were very appropriate.
"Iñaki is dealing with the birth of his son and leaving might upset him a little more, but we have to be careful with our words. Going to Saudi Arabia is prestigious because we're playing for a title and our club receives money to go there.
"We'd all like the fans to be there, but we have to be respectful."
Athletic meet Osasuna in their semifinal playoff this week.
Valverde added: "For now, the goal is to beat Osasuna; I'm not looking beyond that. It's an extremely difficult match against a very strong home opponent. We have to recover the points lost along the way, fighting for them."