This work is devoted to the analysis of inverse problems of permittivity reconstruction of diaphragms loaded in a rectangular waveguide including justification of the solution to a benchmark inverse problem of reconstructing permittivity of a one-sectional diaphragm. We perform comparison of theoretical and numerical results based on the measurement data to validate the efficiency of the proposed technique. The obtained solutions can be implemented in practical measurements for investigation of new artificial materials and media and can be applied in optics, nanotechnology, and design of microwave devices.