The latest information I've seen in Japanese is that 4 have been confirmed dead and two are missing in Kumamoto as a result of last night's downpour:

Japanese source:
http://news.tbs.co.jp/newseye/tbs_newseye2802919.html

-- Kirk

http://www.japantimes.co.jp/news/2016/06/21/national/kumamoto-area-downpours-leave-two-dead-three-missing-trigger-evacuation-advisories/