Kumamoto City had a Level 3 earthquake at 9:39. It felt pretty strong to me but it was only a 3. The magnitude was 3.5. Here’s my Japanese source of information:
http://www.anshin.pref.kumamoto.jp/rireki/saigai/1-21324.html
The Central, East, and West Wards of Kumamoto City and Mashiki and Kashima were at level 3. Surrounding areas were at 2 or lower.
– Kirk