Integral Equation (IE) formulation solved by Method of Moments may be used efficiently to address the problem of quasi-waveguide structures, i.e. structures consisting of a main waveguide with a constant cross section that may bear an arbitrary number of printed circuits backed by dielectric substrates. In the case that the structure as well as the excitation has symmetry requirements, simplifications may be applied on the problem leading to a considerable improvement in the usage of computational resources and time. In this paper we have developed and tested the theoretical formulation to apply the symmetry conditions on the IE technique in the context of shielded multilayered structures excited by waveguide ports. The formulation has been successfully applied to waveguide filters which use frequency selective surfaces as coupling elements.