An accurate and efficient frequency-dependent measurement method is proposed to determine the individual complex permittivities of a two-layered medium. The sample material under test fills only a part of the waveguide cross section, thus a sample with a high-loss layer can be measured without precise machining of the sample material. In this method, which is based on the accurate and numerically efficient hybrid electromagnetic analysis method, only the transmission parameter, , is measured; the complex reflection parameter, , which is difficult to measure, is not required. Virtual experiments demonstrate the efficiency and robustness of the present method. The procedure has a tolerance for variation in initial guess and shows a rapid convergence. Also, investigating the sensitivity of permittivities to deviations in sample location, thickness, and width reveals that the permittivities are largely uninfluenced. Actual experiments are performed at -band with and without the use of calibration to demonstrate the practicality of the proposed method for assessment of the layered sample including a high-loss layer.Index Terms-Layered sample, hybrid electromagnetic (EM) method, inverse problem, permittivity, spectral-domain approach.