The methods are developed for reconstructing permittivity of the inclusion in a rectangular waveguide with perfectly conducting walls by comparing the results of multifrequency measurements of the principal waveguide mode transmission coefficient with the data obtained from numerical solution to Maxwell's equations. Optimal schemes for experimentation and processing of the obtained data are proposed on the basis of comparison of experimental data with closed-form solutions for cases of empty waveguide and the waveguide containing a uniform diaphragm.