Structural planes, such as fractures, bedding planes, schistosity, and so on, induce heterogeneity of permeability field in geologic bodies. One of the ways to demonstrate the heterogeneity is to geostatistically infer the spatial correlation structure. This paper presents a newly developed geostatistical technique for estimating the three-dimensional heterogeneous permeability field. In the presented method, the plane-directional anisotropy of spatial correlation structure of the three-dimensional permeability field is determined by estimating semivariograms in multiplane directions, using limited in situ measurement data of basement rock permeability. A case study of a dam site shows that the spatial correlation of permeability in the direction parallel to the fault planes is greater than that perpendicular to it. Direction of the largest anisotropy of the spatial correlation of the permeability field is concordant with the strike of the major faults.