Thomas Tuchel has claimed he is 'offended deeply as a coach' and dismissed 'baseless' remarks after heated criticism from Uli Hoeness.
Hoeness, Bayern Munich's honorary president, had suggested that the manager doesn't have the willingness or ability to improve his players.
Tuchel is due to leave in the summer and they are in talks with Ralf Rangnick to replace him, but more than 17,000 fans have signed a petition demanding that he stay.
The turmoil between Tuchel and Hoeness does the club no good heading into Tuesday's Champions League semi-final first-leg with Real Madrid.
'It offends me deeply as a coach,' Tuchel said.
Thomas Tuchel has responded to Uli Hoeness' criticism about his attitude, saying he is 'offended deeply as a coach'
Hoeness, Bayern Munich's honorary president, claimed that Tuchel thinks he can't improve players
'If we have proven something in the coaching team over the last 15 years, it is that young players - especially from the academy - always have a place with us in training and, through performance, always have a place on the pitch.
'And by the way, we have now proven that! I have very little understanding of it. I find it absolutely baseless!
'This is actually so far away from reality that I wouldn't have reacted to it at all if it hadn't come from Uli.
'The fact that comes from our boss before Real gives it a different flavour.'
Hoeness, a regular critic of Tuchel, had said: 'He doesn’t think he can improve a Davies, Pavlovic or Musiala. If it doesn’t work, you should buy someone else.
'I think you should work hard on them and give them confidence.'
Hoeness said he expects a coach to 'improve young players.'
The Bayern legend has been making swipes at Tuchel all season.
Tuchel, who leaves this summer, questioned the timing of Hoeness' remarks as a Champions League clash with Real Madrid approaches
Bayern are in talks with ex-Manchester United interim boss Ralf Rangnick to replace Tuchel
After Tuchel complained about squad depth last summer, Hoeness said: 'Those statements are a feast for the media, especially the tabloids.
'Some, including the coach, made unwise statements, because I shouldn't make my own team look bad by saying our squad is too thin. We don't have a thin squad!'
While Bayern have lost out on the Bundesliga title and DFB-Pokal, they can make amends by winning the Champions League.
For anyone thinking the Tuchel-Hoeness spat could destabilise them going into a critical showdown, Thomas Muller offered his blunt thoughts.
'There will be no disturbing noises with us,' he said, revealing that he told club legend Oliver Kahn: 'I don't give a s***.'