The champions and Cup holders suffered a stinging 4-2 defeat at the hands of a youthful and spirited Bayer Leverkusen side on Wednesday, the loss coming hot on the hells of three defeats in five matches since the Bundesliga resumed in January.
Some Bayern fans on Wednesday demanded the resignation of coach Jurgen Klinsmann, in his first season in charge of the team.
"This was the first real blow for us because we are out of one competition," Hoeness told reporters.
"All other things can be repaired. We must be critical with the situation but in no case must we give in to what the media have been trying to do and that is to stir unrest, turn the players against the coach and vice versa."
Bayern have dropped to fifth in the league, four points off the top, picking up only four out of a possible 15 points since the winter break. They take on mid-table Hanover on Saturday.
"I still feel that our present position is not that bad. It makes no sense to start pounding the players. We must motivate them to meet our Bundesliga and Champions League goals. The two biggest aims are still in sight."
Bayern host Sporting Lisbon on Tuesday in the return leg of their Champions League last-16 tie, having won 5-0 in Portugal 5-0 last week.
"We should not stick our heads in the sand now because we would also jeopardise those goals," Hoeness said.
