The Bosnian and a group of friends are accused of clashing with the BayArena stewards following Wednesday's game and video footage allegedly shows the player attacking staff repeatedly after being refused access to a part of the arena.
Leverkusen said police had passed on their report to the prosecutor's office, which has since launched an investigation into the incident.
"Bayer 04 Leverkusen will support all efforts for a full and complete investigation of this incident," they said in a statement.
"Once the club has received the results of the investigation it will also consider internal sanctions. Emir Spahic will -- also on behalf of his group -- apologise in person to the stewards involved."
Spahic, who has been sent off twice in the league this season, has been a defensive stalwart for Leverkusen since joining in 2013 after spells at clubs in Russia, France, Spain and Bosnia.
(Reporting by Karolos Grohmann; editing by Toby Davis)
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