Thomas Mueller has played down fears he could miss Bayern Munich's home Champions League last 16 match against Besiktas in a fortnight after limping out of a German Cup win.

Mueller, Bayern's captain with Manuel Neuer currently injured, badly bruised his thigh colliding with Paderborn's goalkeeper Michael Ratajczak in the build-up to Kingsley Coman's opening goal in a 6-0 cup quarter-final away win on Tuesday.

Mueller played on, but came off after 32 minutes raising fears he could miss Bayern's home Bundesliga match against Schalke this Saturday, plus their key home European match against Besiktas on February 20, with the last 16 return in Istanbul on March 14.

Mueller took to Twitter to allay fans fears.

"The medical staff took good care of me after I was taken off and I will be able to play again soon. No worries! Thanks for all the well wishes," wrote Mueller on the social media platform.

Bayern head coach Jupp Heynckes was more conservative when asked about the health of Germany's forward.

"We'll have to see how things go in the next few days," said Heynckes.

"But we hope that he will be back with us on Saturday - Thomas is a very important man for us."

Mueller is the lynchpin in Bayern's attack and in great form with three goals in his last five Bayern games.

He is due a break after making an appearance in all of Bayern's last 11 games.

The Bavarian giants are 18 points clear in Germany's top flight.

Fifth-placed Schalke are in the pack looking to bridge the gap and hinder Bayern's march to a sixth straight Bundesliga title.