The Germany international has a release clause in the region of £50m in his contract, which has another three years to run.
No concrete offers have been made for Werner yet, but Nagelsmann concedes that the 24-year-old may move on to further his career.
"There is nothing we can do about it," he told reporters. "He knows what he has in Leipzig and also what he has with me.
"I show him that - he gets many chances to develop himself. I don't know if it will help him that much if I tell him every day.
"A player has to feel that he can get better. If he doesn't feel that, it wouldn't do any good if I kept on telling him to stay here.
"In the end, it is his life, his career, he can decide that. I can't think of anything new to say to Timo."
Nagelsmann was speaking after Leipzig's 4-2 win over FC Koln on Monday, with Werner scoring the third of his side's goals.