The goalkeeper fractured his lower right leg in a fall on Friday and has already undergone surgery, with the calamitous setback coming just days after Germany tumbled out of the World Cup in the group stage.
Bayern must decide whether second-choice keeper Sven Ulreich takes over the gloves for the rest of the season, or if Neuer's injury should prompt a move for an elite replacement in the January transfer window.
Ulreich filled in when a shoulder problem kept Neuer sidelined earlier in the season, and Bayern have won all eight games in 2022-23 when the 34-year-old has started, conceding just six goals.
Former Germany Under-21 goalkeeper Alexander Nubel is in the second year of a two-year loan to Monaco, where he has been a first-team regular, and it is not yet known whether Bayern may look to recall the 26-year-old.
Bayern CEO Oliver Kahn said: "The news of Manuel's injury shocked us all. We will stand by him and accompany him on his way to his comeback.
"He will also overcome this serious injury and return to the pitch as strong as before."
In a statement on the club's website, sporting director Hasan Salihamidzic said: "The fact that Manuel had such an accident is terrible, and of course all our thoughts are with him.
"I spoke with him yesterday and today, and the surgery went as well as possible. Manuel will receive all the support he needs.
"He is a strong personality and will come back. I wish him all the best, he can rely on FC Bayern!"
Germany boss Hansi Flick also sent his best wishes, saying: "We wish Manu a speedy recovery!"
Neuer, 36, would have been hoping to play a key role in Bayern's pursuit of silverware in the Bundesliga and Champions League after the World Cup break.
He said the injury occurred while he was "trying to get my head clear" after the misery of Germany's early exit in Qatar.
Bayern face a daunting last-16 clash with Paris Saint-Germain in the Champions League, while they are due to return to Bundesliga action on January 20 against RB Leipzig.
The Bundesliga champions have already signed big-name duo Sadio Mane and Matthijs de Ligt, while the promising Ryan Gravenberch and Noussair Mazraoui have arrived from Ajax.
Speaking at a news conference to present De Ligt to the media after his €80million arrival from Juventus, Kahn revealed he expects there to be further movement.
Teenage Rennes forward Tel, experienced RB Leipzig midfielder Laimer and Germany international Raum have all been linked with a switch to the Allianz Arena.
"We have had further discussions with these players and now we just have to wait and see," said Bayern CEO Kahn on Wednesday.
"The transfer window is still open for a while. Sometimes things move very quickly.
"After analysing last season, we thought we should make a few statements. We want to continue to be among the top four teams in Europe."
Bayern have lost star striker Robert Lewandowski to Barcelona, with the Catalan giants continuing to make significant outlays in the transfer market despite questions about their finances.
Julian Nagelsmann openly questioned the situation at Barca but Kahn was far more cautious on the subject.
"You can't be fooled by all the transfers from Barcelona. I'm not a fan of judging things from the outside," said Kahn.
"None of us can really judge how the situation is. I find that a bit difficult. They'll know what they're doing because they're the only ones who really know the numbers."
The Bundesliga champions and the MLS Cup holders have set up a joint venture named "Red&Gold Football" based in Munich, with the aim of developing players for both teams internationally.
Bayern chief executive Oliver Kahn said the partnership with LAFC will enable Bayern to continue to compete with their European rivals, saying improvements in the quality of MLS will benefit the Bavarian giants.
"On an international level, soccer is developing rapidly, which is also evident in the transfer market," Kahn told the club's website.
"We see this partnership as an opportunity to strengthen FC Bayern in the sporting competition with the best clubs in Europe and the Bundesliga.
"The fact that the 2026 World Cup will largely take place in the United States, where we already have an office in New York, makes Los Angeles even more attractive.
"I expect a boost in quality and young talent in Major League Soccer, which will have a positive impact on our partnership."
LAFC co-president and general manager John Thorrington said: "A partnership of this magnitude is the next step in our evolution as a club. We are extremely excited to work together with FC Bayern to identify and develop young talent in Southern California and beyond.
"We believe this relationship will provide players throughout our systems with the ability to maximise their potential and see a clear pathway to first-team football."
The sides envisage the partnership could grow to include other clubs and development academies across the game in the future "as part of a global development initiative".
Nagelsmann was replaced as head coach by Thomas Tuchel during the international break, with the new boss leading Bayern to a 4-2 win over Bundesliga title rivals Borussia Dortmund in his first game in charge on Saturday.
The 35-year-old was said to have learned of his imminent exit while enjoying a skiing holiday in Austria, with Bayern's decision widely reported 24 hours before it was officially announced.
Bayern sporting director Hasan Salihamidzic denied anyone at the club leaked the news, an assertion that was repeated by Kahn on Saturday.
Speaking to Sky Germany ahead of the win over Dortmund, Kahn referred to Nagelsmann's departure as a "disaster" but insisted the coach was "the first to know" about his sacking.
However, Nagelsmann's management agency Sports 360 has now disputed those claims, saying Bayern did not make contact with the coach before his exit was reported.
"There has been no contact or attempt to get in contact from Bayern," a representative from Sports 360 told Sky Germany.
"After all the rumours in the media, the management of Julian Nagelsmann contacted Hasan Salihamidzic by themselves."
Bayern cruised into a four-goal lead within 50 minutes as they leapfrogged BVB at the Bundesliga summit on Saturday, posting a ninth successive win in home meetings with their Klassiker rivals.
Germany, who were expected to reach the latter stages of Qatar 2022, crashed out at the group stage, leading to the departure of team director Oliver Bierhoff after 18 years.
There was speculation boss Hansi Flick would follow him, but the former Bayern Munich coach confirmed he would be staying on board.
The new advisory group includes former Bayern CEO Karl-Heinz Rummenigge, Oliver Mintzlaff, and former Germany internationals Matthias Sammer, Rudi Voller and Oliver Kahn.
It will be led by Neuendorf and DFB vice-chairman Hans-Joachim Watzke.
"I think this is a group that knows a lot about men's football and the national team," Neuendorf said. "We are not an association in which one person decides everything.
"There will be a first discussion before Christmas. We will give ourselves a timetable there. We have to join forces towards the European Championship in 2024. It has to be a success."
Neuendorf also confirmed there will be a new group that will "take a close look at the entire business area for which Bierhoff was responsible".
This group will include DFB general secretary Heike Ullrich, former Germany international Philipp Lahm and European Championship ambassador Celia Sasic.
"We will see how we set up the area in the future in order to be successful," Neuendorf added. "And we will be self-critical."
