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Germany veteran Neuer is out for the rest of the season after a freak skiing injury sustained during a post-World Cup holiday, with Yann Sommer signed from Borussia Monchengladbach as a replacement.
The arrival of Switzerland international Sommer coincided with the dismissal of long-term Bayern goalkeeping coach Toni Tapalovic, a move Neuer criticised in an interview with The Athletic.
Neuer may leave Bayern after stunning outburst
His comments have sparked widespread backlash, including from coach Julian Nagelsmann, and Germany's most-capped player Matthaus has added his own voice to the chorus of disapproval.
"Manuel Neuer is no longer acceptable as Bayern captain," he said. "He skied negligently and now vehemently attacks the club. Didn't he say a few weeks ago no one was above the club?
"He is an icon of world football, one of the greatest to ever play for Bayern and Germany. I was the biggest fan you can imagine of him, but it is his own fault, the skiing accident and this interview.
"He did his club such a disservice, they have to do without his irreplaceable class for months, maybe even forever, and continue to pay his lavish salary.
"Bayern were more loyal to Neuer than to any other player. Serge Gnabry was publicly thrown at hell and Manuel didn't say a bad word to the outside world.
"Bayern had to sign Yann Sommer for a lot of money and now [they] have to read that they ripped out [Neuer's] heart."
In Neuer's absence, Bayern defeated Wolfsburg on Monday in a 4-2 victory as Nagelsmann's side leapfrogged unlikely title challenger Union Berlin at the Bundesliga summit.