Bayern CEO Karl-Heinz Rummenigge slammed a section of the club's fans who attacked Schalke supporters in violent clashes in Gelsenkirchen on Saturday.
Rummenigge stressed that Bayern "dissociates itself unequivocally" from the "so-called supporters" who were involved in what police described as an "extremely violent attack".
"Violence cannot and should never be tolerated," Rummenigge said in a club statement.
"I expected that fans of FC Bayern appropriately behave sensitively. Almost all have done that, but unfortunately not all, and I am very disappointed."
Rummenigge went on to apologise to Schalke and to those who suffered injuries in the attack.
"Local police responded well considering the difficult situation of escalating violence," he added.
Bayern beat Schalke 3-1 to extend their lead at the Bundesliga summit to eight points, with David Alaba, Javi Martinez and Thomas Muller on target for Pep Guardiola's men.