Scattering in the time domain of electromagnetic waves in the elongated waveguide with 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 for various frequency ranges. Computation for the non-stationary Maxwell equation system is performed by efficient 3D FDTD solver EMWSolver3D created by this paper authors. Simulation is performed for the H10-mode scattering from dielectric slab inclusions. Numerical computations for large-scale problems solution have been implemented on supercomputers of the last generation. The simulation of an empty waveguide without dielectric inclusions has shown that numerical dispersion arising during waves travelling in waveguide causes solution errors. Numerical phase velocity is shown to differ from the analytical phase velocity with the lapse of time that obstructs accurate finding of attenuation and propagation factors. In this respect method similar to Total Field/Scattered field has been proposed to specify waveguide mode with respect to numerical dispersion. The analytical solution of finite-difference equation for the H10-mode has been found for this purpose. Usage of the methods described above has allowed the authors to compute the values of waveguide attenuation and propagation factors for different configurations of dielectric slab.