Germany ran out 5-1 winner against Azerbaijan in their World Cup qualifier on Sunday, but Mustafi did not see out the match and is now set for a lengthy spell on the sidelines.
The Gunners defender pulled up with the injury in the first half and was immediately replaced by Matthias Ginter, with Germany coach Joachim Low revealing afterwards that the injury does not look good.
Arsenal will want to carry out their own examinations, but Low believes the 25-year-old has suffered a tear and is facing a prolonged spell on the sidelines.
"With Mustafi it seems that it is some muscle tear or some muscle fibre tear," Low said after the game. "In any case it could force him to a longer break."