The oedometric compaction of materials with collapsible structure is investigated from a numerical point of view. Such materials form planar zones of localized volumetric deformation that may or may not be accompanied by grain crushing. The purpose of the present work is to investigate the evolution of the permeability and its anisotropy as the result of the formation of compaction bands. The finite element method is used for the simulations with the commercial software ABAQUS. The mechanical response is calibrated on experimental results from the literature. Due to the localization of the deformation, the problem is not numerically stable and shows mesh dependence when a simple material model is used. To resolve the issue a nonlocal formulation is implemented. Drained oedometric tests are simulated. For the permeability different formulations are used, either ignoring the anisotropic evolution of the pore network or accounting for it. The results show that permeability anisotropy at the microscale needs to be considered, because otherwise the predicted reduction in permeability is qualitatively not in agreement with experimental results. On the whole, it is concluded that the permeability reduction following the formation of compaction bands can be highly anisotropic both at the micro and the macro scale.