This paper presents the development of a model enabling the analysis of rarefied gas flow through highly heterogeneous porous media. To capture the characteristics associated with the global- and the local-scale topology of the permeable phase in a typical porous medium, the heterogeneous multi-scale method, which is a flexible framework for constructing two-scale models, was employed. The rapid spatial variations associated with the local-scale topology are accounted for stochastically, by treating the permeability of different local-scale domains as a random variable. The results obtained with the present model show that an increase in the spatial variability in the heterogeneous topology of the porous medium significantly reduces the relevance of rarefaction effects. This clearly shows the necessity of considering a realistic description of the pore topology and questions the applicability of the results obtained for topologies exhibiting regular pore patterns. Although the present model is developed to study low Knudsen number flows, i.e. the slip-flow regime, the same development procedure could be readily adapted for other regimes as well.