Matthias Sammer added that Robert Lewandowski's arrival in the summer is not set to force out the Croatian this month.
The Croat, 27, has been linked with the likes of Juventus and Arsenal after Robert Lewandowski signed 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 its 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 is back in action against Stuttgart on Wednesday and all eyes will be on whether Mandzukic is in the squad as the January transfer deadline days lingers 48 hours later.