Low-permeability rock is suitable as the host rock of an underground repository for radioactive waste disposal; however, minor faults might develop there. Investigating the shear compliance of those faults is crucial because they could be elastically sheared by the thermal effect of the waste to damage the waste’s engineered barriers. This study performed constant-head step-injection tests along with a recently developed packer-pressure-based extensometer method for assessing the applicability of this method to investigate the shear compliance of minor faults. Herein, two neighboring minor faults (A and B) in siliceous mudstone were evaluated. The results showed that fault A, with centimeter-thick fault breccia, exhibited high shear compliance, whereas fault B, with millimeters or less-thick fault breccia, displayed low shear compliance despite containing an incohesive fault rock. An elastic shear displacement occurred for fault A during injection and reached 15–66 mm when the test-section pressure increased from 4.1 MPa to 4.3 MPa. Here, the shear compliance was 101 mm/MPa or more. Conversely, fault B had cohesion, and shear displacement was undetected even when the test-section pressure increased from 4.0 MPa to 6.0 MPa. In this case, the shear compliance was 10− 1 mm/MPa or less. The estimated shear compliances were consistent with the results from previous shear experiments, and therefore, the applied method helps investigate the shear compliances of minor faults.