The Germany international fractured his left foot during Bayern’s defeat to Real Madrid and will spend around eight weeks on the sidelines, CEO Karl-Heinz Rummenigge confirmed. Germany play twice in early June.
Manuel Neuer is "set for a lengthy spell out", Bayern confirmed on the club's official Twitter account, and CEO Karl-Heinz Rummenigge said Germany's number one is expected to miss eight weeks. Neuer had an operation on the same foot just three weeks ago.
Neuer's injury means he misses the Bundesliga run-in and is also set to miss the German Cup final on May 27, should Bayern beat Borussia Dortmund next Wednesday and qualify.
The DFB Pokal is the only competition Bayern have left to play for this season, with the Bundesliga title all but secured and the club now being out of the Champions League after the extra-time defeat away to Real Madrid.
A Bayern statement on Thursday said Neuer would not need a new operation but implied he would miss any Cup final.
"Of course I'm sad I won't be able to help the team in the final spurt of the season. I'm fully focused on recovering as soon as possible. That's the main thing for me now," the 31-year-old said.
Germany also face Denmark in a friendly on June 6 and San Marino in a World Cup qualifier on June 10.
Neuer is likely to now skip those games, giving a chance to the likes of Barcelona shotstopper Marc-Andre ter Stegen.
Neuer's Confederations Cup participation in late June could also be in doubt.