Khedira could be fit for Germany qualifiers
Holding midfielder Khedira was forced to miss the 2-1 friendly win over Uruguay on Sunday and returned to individual training only on Monday.
"With Sami Khedira everything is going according to plan. He trained with the football yesterday and will do it again today. As far as the injury is concerned it has healed," Flick told reporters.
"If he is fit he will play but if we see a risk then it is also our obligation to the player, to be careful. We will know for sure if he can play after Thursday's training."
Germany, who top their Euro qualifying group with five wins from as many matches, travel to Austria on June 3 before taking on Azerbaijan four days later.
With fellow holding midfielder Bastian Schweinsteiger ruled out through injury, Toni Kroos could slip into a more defensive role.
"Toni has played successfully in that position in the past," Flick said.