At higher frequencies, metal loss effects in passive waveguide components become more pronounced and hazardous. In this paper, we propose two integral equation techniques, based on the generalized admittance and impedance matrices, for the accurate consideration of losses in the metal walls of waveguide junctions. Both techniques have been evaluated in terms of accuracy and numerical efficiency, and conclusions are drawn regarding the best properties of the admittance parameter formulation. Finally, combining such technique with a classical perturbative method for considering propagation losses, we have successfully predicted all loss effects in two real waveguide filters used for commercial applications.