Permeability is a fundamental property of porous media. It quantifies the ease with which a fluid can flow under the effect of a pressure gradient in a network of connected pores. Porous materials can be natural, such as soil and rocks, or synthetic, such as a densified network of fibres or open-cell foams. The measurement of permeability is difficult and time-consuming in heterogeneous and anisotropic porous media; thus, a numerical approach based on the calculation of the tensor components on a 3D image of the material can be very advantageous. For this type of microstructure, it is important to perform calculations on large samples using boundary conditions that do not suppress the transverse flows that occur when flow is forced out of the principal directions. Since these are not necessarily known in complex media, the permeability determination method must not introduce bias by generating non-physical flows. A new finite element-based method proposed in this study allows us to solve very high-dimensional flow problems while limiting the biases associated with boundary conditions and the small size of the numerical samples addressed. This method includes a new boundary condition, full permeability tensor identification based on the multiscale homogenization approach, and an optimized solver to handle flow problems with a large number of degrees of freedom. The method is first validated against academic test cases and against the results of a recent permeability benchmark exercise. The results underline the suitability of the proposed approach for heterogeneous and anisotropic microstructures.