Interesting (but small) museum with very well designed exhibits (e.g. the animal dioramas... especially the deer one: when you get upstairs to the history section, look to see what the early hunters are aiming their spears at!).
For a foreign visitor, it was great to learn about regular Japanese life in the past... most of what we see in the west involves Samurai, Emperors and ninjas, so it was very educational and valuable to see what the "normal" people do and did. 20th Century history section was also very interesting to see from a different perspective.
It obviously helps if you can read Japanese as all of the exhibit explanations are in Japanese, but the staff on the front desk were lovely and helpful, and dug out an English overview guide for this struggling gaijin.
Four preserved traditional buildings (approx. 200 years old) outside to view as well, and also located right next to the Miyazaki Jingu shrines.