The present paper deals with the determination of permeability in partially saturated conditions for weakly permeable porous rocks such as argillites or deep clayey formations. The level of permeability can be obtained via the measurements of transient weight loss of a sample submitted to a decrease in relative humidity imposed by saline solution in a hermetic chamber. An identification method based on simplified uncoupled 1D-linear and 1D-non-linear modelling was presented in a previous paper (Giraud et al. Trans Porous Media 69(2):259-280, 2006). The present paper takes into account generalized mass transfer phenomena such as Darcean advective transport of liquid and gas mixtures and Fickean diffusive transport of the vapour specie inside a gas mixture. Poromechanical coupling as well as 3D effects due to the geometry and finite dimensions of the tested samples are also covered by this approach. The coupled THM finite element computer code Code_Aster is then used to model the forward problem. The parameter identification procedure is based upon the solution of an inverse problem. The Levenberg-Marquardt algorithm was used for the problem of minimization. Comparisons between previous simplified 1D modelling and 2D-axisymmetrical coupled modelling show that the former method efficiently provides the correct order of magnitude of the level of permeability or the equivalent storage coefficients. Due to the boundary condition, the real 2D-axisymmetrical geometry of the sample must not be neglected if we are to obtain accurate results.