Mario Gotze is currently at Euro 2016 with Germany
The German World Cup winner has been heavily linked with a move away from the Bundesliga champions this summer.
And reports in Germany suggested Bayern had told Gotze he would not be named in their Champions League squad if he opted to stay at the Allainaz Arena next season.
A club statement read: "It has been reported that FC Bayern has 'threatened' Mario Gotze by stating he would not be nominated to play in the Champions League if he remains at the club.
"FC Bayern Munich has demanded that various media sources cease and desist from reporting false claims."
Chairman Karl-Heinz Rummenigge added: "This is complete fiction.
Mario Gotze - 5 things you need to know
“It remains the case that we will resolutely defend ourselves against all false or even malicious reporting using all legal means available to us."
Gotze, who is currently at Euro 2016 with Germany, has been linked with moves to Liverpool and former club Borussia Dortmund after a frustrating season.
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