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The list is extracted from the Gazetteer of Japan 2007 and subsequent update in March 2018 as avaialable at http://www.gsi.go.jp/ENGLISH/pape_e300284.html

The original 2007 list is taken from https://github.com/nyampire/Gazetteer_JP_2007

Prefecture information comes from http://www.soumu.go.jp/denshijiti/code.html

Just grab the file municipalities.json it has a list of objects with the structure

{
  "code": "011002",
  "name_kanji": "札幌市",
  "name_kana": "さっぽろし",
  "name_romaji": "Sapporo Shi",
  "lat": "43.05",
  "lon": "141.35",
  "prefecture_kanji": "北海道",
  "prefecture_kana": "ほっかいどう",
  "prefecture_romaji": "Hokkaido"
}

The name in romaji will include one of the possible denomination Machi, Cho, Shi, Mura, Ku. Note that Ku is only used for the 23 special wards of Tokyo To that are included even if they're not technically a municipality.

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