Bayern president Hoeness weighed into Die Mannschaft's goalkeeper debate last week when he hit out at the German Football Association for their perceived failure to show adequate support to Neuer, captain of club and country.
Neuer's chief positional rival in the Germany setup, Barcelona
star Ter Stegen, had prompted a public exchange of views when he expressed frustration with a lack of international opportunities.
Hoeness criticized the 27-year-old for his comments and, accusing the media of a coordinating a campaign against Neuer, insisted Bayern would not let their players "be damaged without reason".
That could extend to extreme measures if Joachim Low moves to drop 2014 World Cup winner Neuer.
"Before that happens, we will no longer send players to the national team anymore," Hoeness told Sport Bild
Asked whether he would seek talks with head coach Low, Hoeness replied: "He'll hear what we've said before and his ears will ring."
Refusing to allow members of their squad to represent Germany would leave Bayern open to sanctions.
Under FIFA regulations, clubs are obliged to release players to national teams during international windows and major tournaments.
Neuer, 33, has captained Germany since September 2016.
The Schalke product missed much of the 2017-18 season through injury, enabling Ter Stegen to deputize, but returned in time for the World Cup in Russia and has started each of Germany's six matches in 2019.