| Amami-Oshima Island, Tokunoshima Island, Northern part of Okinawa Island, and Iriomote Island | Natural | 2021 | Not checked yet |
| Ancient Capitals of Asuka and Fujiwara | Cultural | 2026 | Not checked yet |
| Buddhist Monuments in the Horyu-ji Area | Cultural | 1993 | Not checked yet |
| Fujisan, sacred place and source of artistic inspiration | Cultural | 2013 | Not checked yet |
| Gusuku Sites and Related Properties of the Kingdom of Ryukyu | Cultural | 2000 | Not checked yet |
| Hidden Christian Sites in the Nagasaki Region | Cultural | 2018 | Not checked yet |
| Himeji-jo | Cultural | 1993 | Not checked yet |
| Hiraizumi – Temples, Gardens and Archaeological Sites Representing the Buddhist Pure Land | Cultural | 2011 | Not checked yet |
| Hiroshima Peace Memorial (Genbaku Dome) | Cultural | 1996 | Not checked yet |
| Historic Monuments of Ancient Kyoto (Kyoto, Uji and Otsu Cities) | Cultural | 1994 | Not checked yet |
| Historic Monuments of Ancient Nara | Cultural | 1998 | Not checked yet |
| Historic Villages of Shirakawa-go and Gokayama | Cultural | 1995 | Not checked yet |
| Itsukushima Shinto Shrine | Cultural | 1996 | Not checked yet |
| Iwami Ginzan Silver Mine and its Cultural Landscape | Cultural | 2007 | Not checked yet |
| Jomon Prehistoric Sites in Northern Japan | Cultural | 2021 | Not checked yet |
| Mozu-Furuichi Kofun Group: Mounded Tombs of Ancient Japan | Cultural | 2019 | Not checked yet |
| Ogasawara Islands | Natural | 2011 | Not checked yet |
| Sacred Island of Okinoshima and Associated Sites in the Munakata Region | Cultural | 2017 | Not checked yet |
| Sacred Sites and Pilgrimage Routes in the Kii Mountain Range | Cultural | 2004 | Not checked yet |
| Sado Island Gold Mines | Cultural | 2024 | Not checked yet |
| Shirakami-Sanchi | Natural | 1993 | Not checked yet |
| Shiretoko | Natural | 2005 | Not checked yet |
| Shrines and Temples of Nikko | Cultural | 1999 | Not checked yet |
| Sites of Japan’s Meiji Industrial Revolution: Iron and Steel, Shipbuilding and Coal Mining | Cultural | 2015 | Not checked yet |
| The Architectural Work of Le Corbusier, an Outstanding Contribution to the Modern Movement | Cultural | 2016 | Not checked yet |
| Tomioka Silk Mill and Related Sites | Cultural | 2014 | Not checked yet |
| Yakushima | Natural | 1993 | Not checked yet |