The claims came after Bayern crashed out of the Champions League semi-finals at the hands of Atletico Madrid on Wednesday.
According to Bild, Guardiola turned on his medical staff, asking how Atletico had managed to get Diego Godin back on the pitch for Wednesday's game after the key defender had missed the first leg through injury.
Guardiola wants Arteta in 'coaching role' at Manchester City
"At Atletico, Godin quickly came back to fitness. Why can't you lot manage that? Why do injuries last so long for us?" Guardiola said.
Bild said one of the medical staff retorted: "He can't say that, you don't have the right to say that! You have all the players at your disposition. All except (Arjen) Robben and (Holger) Badstuber!"
The newspaper reported that witnesses saw France international Frank Ribery intervene "to avoid the worse".
Guardiola rues another Champions League exit
Guardiola, who joins Manchester City next season, has often had run-ins with the club's medical staff. Noted doctor Hans-Wilhelm Muller-Wohlfahrt left the club in April 2015 after almost 40 years of service once relations with the Spanish coach had cooled.
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