Jurisdiction | Cathedral | Type |
| Fukuoka 福岡 | Cathedral of Our Lady of Victory (Daimyomachi Church)  福岡 (Fukuoka), 福岡県 (Fukuoka), 九州 (Kyūshū), Japan  |  Cathedral |
| Hiroshima 広島 | Cathedral of the Assumption of Mary (Noboricho Church) 広島 (Hiroshima), 広島県 (Hiroshima), 中国地方 (Chūgoku), Japan | Cathedral |
| Kagoshima 鹿児島 | Cathedral of St. Francis Xavier (Xavier Church) 鹿児島 (Kagoshima), 鹿児島県 (Kagoshima), 九州 (Kyūshū), Japan | Cathedral |
| Kyoto 京都 | Cathedral of St. Francis Xavier (Kawaramachi Church) 京都 (Kyoto), 京都府 (Kyōto), 関西地方 (Kansai), Japan | Cathedral |
| Nagasaki 長崎 | Cathedral of the Immaculate Conception (Urakami Church) 長崎 (Nagasaki), 長崎県 (Nagasaki), 九州 (Kyūshū), Japan | Cathedral |
| Nagasaki 長崎 | Basilica of the Twenty-Six Holy Martyrs of Japan (Oura Church) 長崎 (Nagasaki), 長崎県 (Nagasaki), 九州 (Kyūshū), Japan |  Co-Cathedral, Minor Basilica,  World Heritage Site |
| Nagoya 名古屋 | Cathedral of Sts. Peter and Paul (Nunoike Church) 名古屋 (Nagoya), 愛知県 (Aichi), 中部地方 (Chūbu), Japan | Cathedral |
| Nagoya 名古屋 | Former Cathedral of St. Francis Xavier (Daimyoji Church) 犬山 (Inuyama), 愛知県 (Aichi), 中部地方 (Chūbu), Japan |  Former Cathedral |
| Naha 那覇 | Cathedral of the Immaculate Heart of Mary (Kainan Church) 那覇 (Naha), 沖縄県 (Okinawa), 九州 (Kyūshū), Japan | Cathedral |
| Niigata 新潟 | Cathedral of Christ the King (Niigata Church) 新潟 (Niigata), 新潟県 (Niigata), 中部地方 (Chūbu), Japan | Cathedral |
| Oita 大分 | Cathedral of St. Francis Xavier (Oita Church) 大分 (Ōita), 大分県 (Ōita), 九州 (Kyūshū), Japan | Cathedral |
| Osaka–Takamatsu 大阪高松 | Cathedral of the Immaculate Conception of the Blessed Virgin Mary (Tamatsukuri Church) 大阪 (Osaka), 大阪府 (Ōsaka), 関西地方 (Kansai), Japan | Cathedral |
| Osaka–Takamatsu 大阪高松 | Co-Cathedral of the Assumption of the Blessed Virgin Mary (Sakuramachi Church) 高松 (Takamatsu), 香川県 (Kagawa), 四国 (Shikoku), Japan |  Co-Cathedral |
| Osaka–Takamatsu 大阪高松 | Former Cathedral of St. Therese (Shukugawa Church) 西宮 (Nishinomiya), 兵庫県 (Hyōgo), 関西地方 (Kansai), Japan |  Former Cathedral |
| Saitama さいたま | Cathedral of St. Theresa of the Child Jesus (Urawa Church) 浦和 (Urawa), 埼玉県 (Saitama), 関東地方 (Kantō), Japan | Cathedral |
| Sapporo 札幌 | Cathedral of the Guardian Angels (Kitaiciho Church) 札幌 (Sapporo), 北海道 (Hokkaidō), 北海道 (Hokkaidō), Japan | Cathedral |
| Sapporo 札幌 | Church of Our Lady of the Immaculate Conception (Motomachi Church) 函館 (Hakodate), 北海道 (Hokkaidō), 北海道 (Hokkaidō), Japan | Former Cathedral |
| Sendai 仙台 | Cathedral of Sts. Peter and Paul (Motoderakoji Church) 仙台 (Sendai), 宮城県 (Miyagi), 東北地方 (Tōhoku), Japan | Cathedral |
| Tokyo 東京 | Cathedral of St. Mary of the Immaculate Conception (Sekiguchi Church) 東京 (Tokyo), 東京都 (Tōkyō), 関東地方 (Kantō), Japan | Cathedral |
| Tokyo 東京 | Former Cathedral of St. Joseph 東京 (Tokyo), 東京都 (Tōkyō), 関東地方 (Kantō), Japan | Former Cathedral |
| Yokohama 横浜 | Cathedral of the Sacred Heart (Yamate Church) 横浜 (Yokohama), 神奈川県 (Kanagawa), 関東地方 (Kantō), Japan | Cathedral |
