Wikipedia (yes, I know the warnings) lists ¥1000, ¥2000, ¥5000 and ¥10,000 as the currently issued banknotes and has nothing higher. https://en.wikipedia.org/wiki/Banknotes_of_the_Japanese_yen
The coins are ¥1, ¥5, ¥10, ¥50, ¥100 and ¥500.
When I was there there were no 2,000 yen notes. I thought there were 50,000 and 100,000 but I could be wrong.