Wave propagation in a waveguide of rectangular cross section with perfectly conducting wall containing an inhomogeneous dielectric insert in the form of a parallel-plane diaphragm with an inclusion is simulated numerically. The permittivity of the inclusion is a quantity to be restored from as little information about the scattered field as possible using FDTD numerical solution of Maxwell’s equations with nonlocal multimode scattering boundary conditions. The optimal number of higher-order evanescent waves and the size of the computational waveguide domain are found using the series of numerical experiments.