Fati has successfully recovered from his injury and made a comeback in the Champions League match against AS Monaco this week.
Ahead of Sunday's trip to Villarreal, Flick said, "I've spoken to him and he prefers to play as a left winger.
"I agree, but he can also play as a centre forward, he's very good with the ball. I've seen a very different Fati to the one who was at Brighton.
"You can see the quality in him. I think he needs more time, we have to look after him."