Bayern Munich's long-time team doctor Hans-Wilhelm Mueller-Wohlfahrt has surprisingly resigned following their Champions League loss to Porto, saying the medical department was blamed for the defeat.

Mueller-Wohlfahrt, a respected doctor, has been in charge since 1977 and has also treated many other top global athletes, including sprinter Usain Bolt, while also being the German national soccer team doctor as well.

"After the Champions League game at Porto for unexplained reasons it was the medical department that was chiefly blamed for the defeat," Mueller-Wohlfahrt said in a late night statement on Thursday.

He said "the relationship of trust has been permanently damaged."

Bayern have been struggling with injuries in recent weeks with Bastian Schweinstieger, Franck Ribery, Arjen Robben and David Alaba all missing the game against the Portuguese team on Wednesday.

The ties with Pep Guardiola who took over in 2014 were tense from the first season with midfielder Thiago Alcantara being sent for treatment to Barcelona by the Spanish coach without consulting the team doctor.

The most recent incident was involving Ribery. The player was initially ruled out for a few days with an injury but the winger has already missed the last five weeks.

"Ask the team doctor, I have no idea," Guardiola said last week when asked when the player would make his comeback.

Mueller-Wohlfahrt's resignation comes at a crucial time for Bayern, who are chasing a treble of titles, entering the crucial phase of the season.

Bayern, who are 10 points clear at the top of the Bundesliga, face Borussia Dortmund in the German Cup last four and have to overturn the 3-1 deficit against Porto in the return leg in Munich next week.

The club could not be immediately reached for a comment.

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