There has been talk of Nagelsmann returning to Bayern for a second spell in charge next season. But he has now penned a new deal with the German Football Federation to 2026.
"I think it's a shame," said Hoeness, though later said sarcastically: "The world is not coming to an end at FC Bayern because of this."
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Hoeness did not want to reveal any information about the current status of Bayern's new coach search.
Referring to sports director Max Eberl and sports director Christoph Freund, Hoeness said: "That is not my job. You have to ask them both, they are responsible for the sport."