Sediment lithology, especially the clay mineral fraction, is basic geologic information, which is important for understanding faulting and evolutionary process of the accretionary prism. During scientific drilling, the clay mineral fraction is measured using X-ray diffraction analyses of samples from the acquired cores. However, coring in an accretionary prism is sometimes difficult, which hinders the acquisition of clay mineral fraction data. This study details the development of a new method used to empirically estimate the clay mineral fraction from the electrical resistivity and natural gamma ray logs obtained from the Kumano section of the Nankai Tough, where multiple scientific drilling expeditions have been conducted. This method is composed of two steps. First, porosity is estimated using electrical resistivity logs. In order to compensate for the effect of porosity, the natural gamma ray logs are then normalized using (1 − porosity). Second, the normalized natural gamma ray logs are converted into clay mineral fractions using an empirical conversion function. This empirical function was determined by comparing all available normalized natural gamma ray logs and clay mineral fractions data collected from the Kumano section of the Nankai Trough. As a byproduct of the porosity estimations, thermal conductivity and temperature depth profiles were also estimated for all of the logging sites. As electrical resistivity logs and natural gamma ray logs are essential measurements made during scientific drilling, this new method can be applied to future drilling expeditions in the Nankai Trough. Although the empirical conversion function established in this study is valid only at the Kumano section of the Nankai trough, the same procedure can be applicable to other subduction zones to establish local empirical conversion functions if enough data are available. The clay mineral fraction depth profile estimated using this method can provide useful information for various geological studies, including sedimentology and structural geology of the shallow accretionary prism.