jun, I can confirm that E6 is still in relatively heavy use in Japan. At least compared to other countries.
Almost every convenience store or train station kiosk carries disposable c-41 cameras and Superia 400, but more serious photographers seem to prefer E6 here it seems. I went to a few camera stores to get film around Mt. Fuji and around Nikko and most of what they carried was E6. Furthermore, in Tokyo they have E6 only labs like "CREATE" in Ginza and Shinjuku. You can still get your slide film developed in 1 hour for 750 yen!
Almost every convenience store or train station kiosk carries disposable c-41 cameras and Superia 400, but more serious photographers seem to prefer E6 here it seems. I went to a few camera stores to get film around Mt. Fuji and around Nikko and most of what they carried was E6. Furthermore, in Tokyo they have E6 only labs like "CREATE" in Ginza and Shinjuku. You can still get your slide film developed in 1 hour for 750 yen!