The 23-year-old returned to training with the Bundesliga champions this week after spending around seven months out of action with an ankle injury.
However, the Spain international has suffered a damaging setback as he prepares to undergo surgery.
Bayern wrote on their Twitter page: "Devastating: @Thiago6 has suffered a ligament tear in training. He needs an operation and is set for another lengthy absence."
Alcantara completed his first full training session on Monday following his initial injury layoff.