Each modern Japanese prefecture has a unique flag, most often a bicolour geometric highly stylised design (mon), often incorporating the characters of the Japanese writing system and resembling minimalistic company logos. A distinct feature of these flags is that they use a palette of colours not usually found in flags, including orange, purple, aquamarine and brown.

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Some prefectures also have alternative official flags called "symbol flags" (シンボル旗). They may be used on less formal occasions. Famous symbol flags include the one used in Tokyo.

• Aichi Prefecture
• Akita Prefecture
• Aomori Prefecture
• Chiba Prefecture
• Ehime Prefecture
• Fukui Prefecture
• Fukuoka Prefecture
• Fukushima Prefecture
• Gifu Prefecture
• Gunma Prefecture
• Hiroshima Prefecture
• Hokkaido
• Hyōgo Prefecture
• Ibaraki Prefecture
• Ishikawa Prefecture
• Iwate Prefecture
• Kagawa Prefecture
• Kagoshima Prefecture
• Kanagawa Prefecture
• Kōchi Prefecture
• Kumamoto Prefecture
• Kyoto Prefecture
• Mie Prefecture
• Miyagi Prefecture
• Miyazaki Prefecture
• Nagano Prefecture
• Nagasaki Prefecture
• Nara Prefecture
• Niigata Prefecture
• Ōita Prefecture
• Ōita Prefecture (variant)
• Okayama Prefecture
• Okinawa Prefecture
• Osaka Prefecture
• Saga Prefecture
• Saitama Prefecture
• Shiga Prefecture
• Shimane Prefecture
• Shizuoka Prefecture
• Tochigi Prefecture
• Tokushima Prefecture
• Tokushima Prefecture (variant)
• Tokyo
• Tottori Prefecture
• Toyama Prefecture
• Wakayama Prefecture
• Yamagata Prefecture
• Yamaguchi Prefecture
• Yamanashi Prefecture

• Symbol mark flag of Kagoshima Prefecture
• Symbol mark flag of Tokyo

• Toyama Prefecture (1957–1988)
• Osaka Prefecture (1968–1984)
• Kumamoto Prefecture (1960)
• Yamagata Prefecture (1963–1971)
• Fukushima Prefecture (1951–1968)
• Ibaraki Prefecture (1966–1991)
• Ehime Prefecture (1989–1999)
• Nagasaki Prefecture (1991, unofficial)
• Karafuto Prefecture (1911–1949)

• Flag of Japan
• List of Japanese flags
• Prefectures of Japan