We have developed a new algorithm of uncertainty analyses for the permittivity calculation of high-loss materials using the Transmission/Reflection (T/R) method. In the T/R method, there are several calculation procedures to derive the permittivity. In our method, the permittivity is derived from measured S-parameters by solving an equation in which S-parameters are included by the form: (S21+S12)+β(S11+S22), where β is a weighted factor to be optimized in order to minimize the uncertainty. We compared uncertainties of the permittivity derived from different calculation procedures to confirm the efficacy of our method. We also proposed a simplified verification method for measurement results.