The Germany international has suffered thigh damage in training and could be facing a significant stint on the sidelines as a result
The 27-year-old picked up a problem in his left thigh in training in Madrid shortly before departing to join up with the Germany squad for their international clashes over the next week, according to the German Football Federation.
Both Madrid and the DFB have since confirmed that Khedira has undergone scans on the problem which kept him out of training with Joachim Low's side.
The Bernabeu side claim, however, that the player suffered the problem while with the Germany squad, contradicting the statement from the DFB, which said the injury occurred before he joined up with the camp.
Initial reports in Germany and Spain suggest the player could be out for six to eight weeks, although neither the world champions nor Madrid have confirmed the severity of the injury as yet.
Germany take on Argentina in a friendly on Wednesday before beginning their Euro 2016 qualifying campaign against Scotland on Sunday.