The 61-year-old says that the team are not performing at a level befitting of the club and is worried their poor results could affect their Champions League campaign
Pep Guardiola's side's had put together a 53-match unbeaten Bundesliga run but suffered back-to-back losses after sealing the German title.
And Hoeness, whose brother Uli was club president until his imprisonment in March, says recent performances are not becoming of the European champions.
"This is not Uli's style, and it's not Bayern's style," he told Sport1.
"It leaves an unprofessional impression and that doesn't fit into Bayern, who are a highly professional club.
"Everyone can imagine how unhappy Uli, who always wants to win, was when Bayern lost against Dortmund."
The 61-year-old went on to suggest their loss of league form could affect their defence of the Champions League and DFB-Pokal titles.
"As a play, you need rhythm in order to deliver your top performances. At least now, after the 3-0, Guardiola will change his preparation."