The accurate hydraulic characterization of low permeability geologic environments has important practical implications. In the present study, we clarified some major problems in using conventional laboratory methods for testing low permeability geological materials. A new and versatile laboratory system is devised that can implement any of the three test methods, the constant-head, flow-pump and transient-pulse tests, while subjecting a specimen to high confining pressures and pore pressures, thereby simulating in situ conditions at great depths. To exam the capabilities of this new laboratory system, a series of cross-check permeability tests is also performed on Shirahama sandstone and Inada granite that are two rock types widely encountered in Japan. The results showed that the permeabilities derived from the three complementary laboratory methods are in general agreement with variations in the same order. The consistency of these results illustrates the versatility and effectiveness of the new laboratory system for testing low-permeability geological materials.