According to Sport Bild, Hoeness warned the German FA that the fight for the first-choice goalkeeping spot could have dramatic consequences for them.
He reportedly said Bayern "will never accept a change of guard" in the national team's goal following the 3-0 Champions League win against Red Star last Wednesday.
When asked about Ter Stegen potentially replacing Neuer as Germany's No. 1, Hoeness was quoted as saying: "If that happens, we will no longer release players for the national team."
However, Hoeness' words ring hollow because FIFA regulations stipulate that "clubs are obliged to release their registered players [...] if they are called up."
Following the last international break, Barcelona goalkeeper Ter Stegen said that not playing in the Euro 2020 qualifying games against Netherlands and Northern Ireland was a "massive blow" and Neuer responded by describing the comments as not helpful.
Bayern president Hoeness then attacked Ter Stegen and the German FA, instructing them to "put Ter Stegen in a corner and make him apologise to Neuer."
At the weekend, Germany coach Joachim Low, attending a Bundesliga match in Freiburg, told reporters that "something like that won't have any influence on me."