In developing or utilizing the shallow/deep geothermal resources, it is no doubt that crustal permeability is one of the most essential parameters and should be carefully explored. However, to date, there is no past research which systematically summarized the crustal permeability data in Japan, despite a number of hydraulic tests have been conducted for the purposes of geo-energy use, groundwater use, civil engineering use, and so on. In this study, we collect and organize crustal permeability data measured/estimated in the various fields of Japan. Crustal permeability data include measurement location, vertical depth (z [km]), rock type, measuring/estimating method, and so on. Based on the collected data, we present the relationship between crustal permeability (k) and depth in Japan. k-z profile of Japan is compared with that estimated from the crustal permeability data around the world (i.e., global k-z profile) (Kuang and Jiao, 2015), and the followings are suggested. (1) Most of the crustal permeability data in Japan are included in the range of upper and lower bounds of the global k-z profile, and (2) Crustal permeability of from shallow to mid-deep part of Japan tend to be slightly higher than the average global k-z profile as a whole. The latter may suggest that crustal permeability is enhanced in Japan, since Japan is located at the plate convergence boundary and is influenced by the disturbances, such as crustal faults, thermal convection by volcanic/geothermal activities, and orogenic processes, a lot. Though there is room for debate about the policy of making database and the differences in data quality, we successfully present the essential charts which can constrain various analysis for the use of geothermal resources. In the future, it is desirable that domestic crustal permeability database, which covers all crustal permeability data in Japan and can be easily accessed by all interested persons, will be released.