Flag of Fukuoka. Stylised hiragana of ふく (fuku). Also represents ume (plum), the prefectural flower.
Flag of Gifu. Stylised kanji 岐 (gi). The emblem expresses peace and harmony. Green for the nature of Gifu.
Flag of Ibaraki. The prefectural flower rose on blue field. Blue for the Pacific Ocean and Mount Tsukuba.
Flag of Kagawa. Stylised and slightly rotated katakana of カ (ka). Also represents mountains, and leaves of the olive, the prefectural tree.
Flag of Kyoto. Stylized kanji of 京 (kyō).
Flag of Miyagi. Stylised hiragana of み (mi). Also represents the miyaginohagi (lespedeza), the prefectural flower.
Flag of Tottori. The symbol represents the hiragana と (to) and a bird (tori) to form a rebus of Tottori.
All prefectural flags are on Wikipedia.
Below the level of prefectures are the municipalities. They also have flags with nicely considered symbolism and, for the most part, appropriate restraint.