Propagation in the time domain of electromagnetic waves in a rectangular waveguide with a non-uniform dielectric slab is considered. Electromagnetic field components are computed and investigation of energy transport in the guide is performed by using Finite Difference Time Domain (FDTD) method in different frequency ranges. Parallel high performance FDTD solver, based on Maxwell equations approximation in integral form on Yee lattice and developed by the paper authors is used. A method for calculating the transmission coefficient with respect to all the problem parameters is proposed. The method is based on the analysis of the amplitude of the scattered wave derived from FDTD numerical solution. The pure scattered field method is proposed to specify the waveguide mode with respect to numerical dispersion. Computations for nonstationary Maxwell equations system are performed for the H10-mode scattering from a dielectric slab placed in the waveguide. Multiple numerical computations for the corresponding large-scale problems have been performed on Lomonosov Moscow State University IBM BlueGene/P supercomputer. Using the methods described above, we compute the values of the waveguide transmission, attenuation and propagation factors in a wide range of permittivity and different positions of the dielectric slab inclusions. Continuous curves on the complex plane describing the dependence of the transmission coefficient on the dielectric constant are obtained. The comparison of the transmission coefficient calculated by the present approach and the volume integral equation method is performed.