The German club's sporting director Matthias Sammer insists Robert Lewandowski's arrival in the summer will not force the Croatian to move this month
The Croat, 27, has been linked with Juventus and Arsenal following Robert Lewandowski signing a deal to leave Borussia Dortmund for the Allianz Arena at the end of the season.
Mandzukic was left out Pep Guardiola's squad for their 2-0 win over Borussia Monchengladbach on Friday and Sammer insisted that his poor showing during the winter break - and not an imminent departure due to Lewandowski's arrival in July - is the reason for his absence.
"Mario has not trained hard enough," the Roten's sporting director told Sky. "The coach decided not to put him in the squad.
"He is precious to us, because he works like an animal. But he has not been doing it this time, so his absence is the consequence.
"It has nothing to do with Lewandowski. He is absolutely not leaving in January."
Bayern are back in action against Stuttgart on January 29 and all eyes will be on whether Mandzukic is in the squad as the January transfer deadline days lingers 48 hours later.