The Allianz Arena chief is gutted for the Germany international, who is not expected to feature again for the Bavarians this calendar year
The 29-year-old is set to undergo surgery on his right ankle for the second time this year after a summer operation failed to solve the problem.
"For Bastian it is very bad, he had only just been back fighting fit again," the 61-year-old told TZ. "And now he gets this setback - it's a catastrophe.
"Bayern can compensate in his absence though."
The reigning Bundesliga champions are still unable to confirm an official date when the Germany international will be ready to return, with sporting director Mathias Sammer revealing his treatment is still under discussion.
"There are still discussions to be had between the player and the physician on the operation," he said. "And then Bayern have to meet to make decisions: where, when and how."
Bayern will return to action after the international break with a crunch match at Borussia Dortmund on November 23.