Lattice Boltzmann method (LBM) has been applied to predict flow properties of porous media including intrinsic permeability, where it is implicitly assumed that the LBM is equivalent to the incompressible (or near incompressible) Navier-Stokes equation. However, in LBM simulations, high-order moments, which are completely neglected in the Navier-Stokes equation, are still available through particle distribution functions. To ensure that the LBM simulation is correctly working at the Navier-Stokes hydrodynamic level, the high-order moments have to be negligible. This requires that the Knudsen number (Kn) is small so that rarefaction effect can be ignored. In our study, we elaborate this issue in LBM modeling of porous media flows, which is particularly important for gas flows in ultra-tight media. The influence of Reynolds number (Re) on the intrinsic permeability is also discussed.