The heavy rain has caused "sediment disaster alerts" (warnings about landslides) to be issued and evacuations called for in various parts of Kumamoto, particularly, but not restricted to, the Aso area. The evacuations I am aware of are:

Minami Aso Mura: 4721 households
Mifune Machi: 7091 households (entire area)
Many parts of Aso Shi
Gyokuto Machi (near Tamana): 1986 households

The information about evacuations that I have comes from
http://www.anshin.pref.kumamoto.jp/osirase/index.cgi?type=1001

The two images have have shared in this post come from
http://www.jma.go.jp/en/doshamesh/349.html?areaCode=349
and
http://www.bousai.pref.kumamoto.jp/GmnDsp.exe?M100A0S0N1P0