In the measuring process of the cavity resonance perturbation method to evaluate permittivity, it has historically been supposed that Q-factor of the cavity itself is not affected by the installation of a sample since the method has been proposed. Recently, several experimental results to show the change of Qfactor by the installation of a sample were found. Measurements and discussions to confirm the change have been made and a method to obtain the intrinsic loss factor of the sample separated from Q-factor change of the cavity is proposed in this paper.