Heynckes will leave Bayern when his contract expires at the end of the season, making way for Pep Guardiola.
He is yet to confirm whether he will retire, and Schalke is reported to be a front-runner for his services.
Hoeness, however, "cannot imagine it in the slightest"."That's got to be a bit of an April's Fool," the Bayern president said in an interview with Kicker magazine.
Schalke director of sport
"We have nothing more to say about it," Heldt said.
Heynckes, 67, coached Schalke for little over a year before being dismissed in 2004.
He then had spells with Borussia Monchengladbach, Bayer Leverkusen and Bayern, twice, and he is on course to lead the Bavarian club to a record 22nd Bundesliga title.
Bayern is also aiming for an historic treble, chasing the DFB-Pokal and UEFA Champions League titles.
Bayern meets Borussia Dortmund in the last eight of the domestic cup and faces Arsenal in the last 16 of the Champions League.