"Why would he leave? He has a contract. He will stay whatever happens," Hoeness is quoted as saying.
Heynckes, 67, had left his future open to doubt in comments made after Bayern lost 3-2 to the Dutch national team in a friendly on Tuesday.
"I have a contract until 2013. If anything changes, we will let you know," he replied when pressed by a journalist.
Several weeks ago, Bayern chairman Karl-Heinz Rummenigge had hinted that Heynckes, who was appointed as coach for a third time last year, would be offered an extension to his deal.
However, since then Bayern have suffered setbacks in losing the German Cup final 5-2 to Borussia Dortmund - who also edged them in the championship - and then losing on penalties to Chelsea in last Saturday's Champions League final at their own Allianz Arena.
(For more sports news and updates, follow Ahram Online Sports on Twitter: @AO Sports)