The 61-year-old says that the team is not performing at a level befitting of the club and is worried the poor results could affect the 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.
Hoeness, whose brother Uli was club president until his imprisonment in March, says recent performances are not becoming of the European champion.
"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 the loss of league form could affect the team's defense 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."