The former France youth international, who joined Bayern from Galatasaray in January for 30 million euros, had previously torn his left hamstring in mid-February.
"FC Bayern will be without full-back Sacha Boey for the next few weeks," the club said in a statement.
"The new arrival this winter suffered a torn muscle in his left hamstring during training on Wednesday. The diagnosis was confirmed by the FC Bayern medical unit."
The Frenchman has made two appearances for the German giants, as a substitute in their 3-1 home win against Borussia Monchengladbach on February 3rd and starting a week later as they lost 3-0 at Bayer Leverkusen.
Goalkeeper Manuel Neuer suffered a muscle strain in his left adductor on international duty with Germany, Bayern added later on Wednesday, while winger Kingsley Coman and defender Noussair Mazraoui returned to training on Tuesday.