A man told me, "You are not Japanese."
But, I'm Japanese.
Which can I reply to him?
"Yes, I'm Japanese." or "No, I'm Japanese."

Question

Answer

Neither. The tone is important here.

Examples:

A: You’re not Japanese? (A thought you were Japanese, but then doubted his belief)
B: I am. 
B: No, I am.

A: You’re not Japanese. (A incorrectly thinks you’re not Japanese)
B: Yes I am. 
B: Yes I definitely am. (Refuting him. You are definitely Japanese)

Answer

The first one