Sporting director Christoph Freund confirmed the Japan centre-back would miss "two to three weeks", ruling him out of Saturday's trip to Borussia Dortmund and putting him in doubt for Bayern's Champions League tie with Atalanta in March.
Ito, 26, has had a torrid time with injuries since arriving at Bayern from Stuttgart in 2024.
He played just six Bundesliga games in his first season after fracturing a bone in his foot and missed the first 10 games of this campaign with another foot injury.
Ito has played 26 matches for Japan, scoring once.