Muller has been with the Bavarians since 2008 and scored 161 goals in 400 appearances in all competitions for the Bundesliga giants.
However, the 28-year-old was benched a few time towards the end of last season and does not seem suited to coach Carlo Ancelotti's preferred system.
This season has begun in similar style as he started in the opening-day win over Bayer Leverkusen but was on the bench for the victory over Werder Bremen a week later.
The Germany international was restored to the starting line-up for the loss to Hoffenheim before again being dropped for the Champions League win over Anderlecht earlier this week.
Hitzfeld feels it is a sign of things to come under the Italian tactician.
"It will be difficult for Muller when the season gets going," he told Focus. "Ancelotti has sent a signal. When the big games come, you know who's going to be playing."