A method for the accurate calculation of the cut-off wavenumbers of a waveguide with an arbitrary cross section and a number of inner conductors is demonstrated. Concepts of integral and infinite-matrix (summation) operator-valued functions depending nonlinearly on the frequency spectral parameter provide a secure basis for formulating the spectral problem, and the Method of Analytical Regularization is employed to implement an effective algorithm. The algorithm is based on a mathematically rigorous solution of the homogeneous Dirichlet problem for the Helmholtz equation in the interior of the waveguide, excluding the regions occupied by the inner conductor boundaries. A highly efficient method of calculating the cut-off wavenumbers and the corresponding non-trivial solutions representing the modal distribution is developed. The mathematical correctness of the problem statement, the method, and the ability to calculate the cut-off wavenumbers with any prescribed and proven accuracy provide a secure basis for treating these as “benchmark solutions”. In this paper, we use this new approach to validate previously obtained results against our benchmark solutions. Furthermore, we demonstrate its universality in solving some new problems, which are barely accessible by existing methods.