The former Germany international has lashed out at the Roten chief after he claimed that the ex-Stuttgart forward was "good, but not very good"
At the end of July, Hoeness appeared to question the 27-year-old's ability by claiming that if he were a truly exceptional player, die Roten would already have won the Champions League.
Sammer did not take too kindly to his chairman's remarks, and believes that the much-maligned hitman should be given more support.
"His [Hoeness'] words are not very good to hear," the former Germany international told Bild. "We must aim to give Gomez more confidence instead.
"The president might have full privileges and a personality that has left its mark on our club but, as he says, if we want to make the step up from good to very good, we must be consistent throughout the organisation.
"Gomez will continue featuring for us, although he naturally must provide evidence of his contributions."
The Bavarian club have brought in Claudio Pizarro and Mario Mandzukic this summer to provide competition for the former Stuttgart player.