The 25-year-old suffered a second metatarsal fracture in his right foot during a 3-2 Bundesliga win over St. Pauli in March, with reports indicating he may not return until early 2026.
Ito, who joined Bayern from VfB Stuttgart in the summer of 2024 for a reported 23.5 million euros, has endured a torrid debut season.
His first metatarsal fracture, sustained in a pre-season friendly against FC Duren, delayed his competitive debut until February 2025, when he featured in a 2-1 Champions League victory over Celtic.
The recurrence of the injury, confirmed by Bayern's medical team, has forced the club to adopt a cautious approach to his recovery. "The news of another serious injury to Hiroki hits us all very hard," said Bayern board member for sport Max Eberl.
"He's only just battled back after months of rehab and will now be out for a long time again."
The injury compounds Bayern's defensive woes, with Alphonso Davies and Dayot Upamecano also sidelined by long-term injuries.
The departure of Eric Dier, confirmed by Bayern recently, further thins their backline.
Sporting director Christoph Freund acknowledged the challenge, stating, "We now have to monitor the injury situation, exactly how long Hiroki Ito will be out."
He hinted at potential moves in the transfer market to bolster the squad. Bayern's versatile defender, capable of playing centre-back or left-back, was seen as a key piece in Vincent Kompany's tactical setup, making his absence a significant blow.