The permeabilities of fault rocks from the rupture of Wenchuan earthquake were measured by using nitrogen gas and distilled water as pore fluids under the confining pressure ranging from 20 to 180 MPa at room temperature. Experimental results indicate that both gas and water permeabilities decrease with increasing confining pressure, described by power law relationship, i.e., b = 0.2×10-3kl-0.557. The water permeability is about one order less than gas permeability and also half order smaller than the permeability corrected by the Klinkenberg effect, so-called intrinsic permeability. The differences in the permeabilies imply that the reduction of effective pore size caused by the adhesion of water molecules to clay particle surface and waterswelling of expandable clay minerals contributes to lessening the water permeability besides the Klinkenberg effect. Hence, the liquid permeability of fault rocks cannot be deduced by gas permeability by the Klinkenberg correction reliably and accurately, and it is necessary to use liquid as pore media to measure their transport property directly.