Hoeness put forth his doubt over Gomez's abilities as a genuinely world class striker last month, when he claimed that the Germany international is "not very good".
However, Sammer believes that Hoeness was wrong to publicly attack the 27-year-old and says that Gomez should be given more support by everyone at the club.
"His (Hoeness's) words were not very good to hear," he told Bild. "We must try 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 must provide evidence of his contributions."
Gomez scored 26 goals for Bayern in the Bundesliga last season, as the Bavarian giants finished second behind Borussia Dortmund.