In the construction of a deep underground facility, the hydromechanical properties of the rock mass around an underground opening are changed significantly due to stress redistribution. This zone is called an excavation damaged zone (EDZ). In high-level radioactive waste disposal, EDZs can provide a shortcut for the escape of radionuclides to the surface environment. Therefore, it is important to develop a method for predicting the detailed characteristics of EDZs. For prediction of the EDZ in the Horonobe Underground Research Laboratory of Japan, we conducted borehole televiewer surveys, rock core analyses, and repeated hydraulic conductivity measurements. We observed that niche excavation resulted in the formation of extension fractures within 0.2 to 1.0 m into the niche wall, i.e., the extent of the EDZ is within 0.2 to 1.0 m into the niche wall. These results are largely consistent with the results of a finite element analysis implemented with the failure criteria considering failure mode. The hydraulic conductivity in the EDZ was increased by 3 to 5 orders of magnitude compared with the outer zone. The hydraulic conductivity in and around the EDZ has not changed significantly in the two years following excavation of the niche. These results show that short-term unloading due to excavation of the niche created a highly permeable EDZ.