Sendai, Miyagi (1933)
Hida, Gifu
Kawasaki, Kanagawa (1925)
Hiroshima, Hiroshima (1896)
Kitami, Hokkaido (1947)
Kochi, Kochi (1920)
Naruto, Tokushima (1947)
From this list of Japanese municipal flags (split into regions).
A few of the designs are briefly explained over on Pink Tentacle. Biei’s symbol, for example, features the hiragana び (bi) in the shape of Mt. Tokachi.
Biei, Kamikawa
Via Design Observer.