The midfielder comes off contract at the end of the season and is interesting Barcelona, Real Madrid, Liverpool and Manchester City.
Eberl told Sky Deutschland: "In general, no one is above the club, and if a player decides differently, he decides differently. And then Bayern will continue anyway."
On Bayern's offer to renew Kimmich, which was later withdrawn, Eberl confirmed: "Yes, it's public knowledge. If the truth is public, that's it. We're negotiating, we're talking. We've never given a position on how the negotiations are going. We talk among ourselves and that's the most important thing."
On whether patience in the Kimmich case was the wrong tactic, he also said: "We'll see when the result is in. When the result is ready, then you can cast your vote (referring to the media)."
As for the possibility that the management felt cheated by the player, Eberl concluded: "No, we don't feel cheated at all by Joshua Kimmich. Joshua is playing an extraordinary season, he's had an incredible performance so far. At the club we all know what we have with Joshua. Is the relationship with us intact? Absolutely."