An unidentified Fomitiporia sp. initially identified as Fomitiporia punctata, causes severe trunk sap rot on Cryptomeria japonica cultivar “Sanbu-sugi”. We investigated the physiological characteristics of the mycelia of the causal fungus (F2, F6, and F43), in comparison with F. punctata (Fp) as a reference, in eight different experiments. The three unidentified isolates showed similar tendencies in change in mycelial growth during incubation, optimal growth temperatures (25 °C), optimal pH range (pH 5–6), glucose to yeast extract ratio (45), utilizable carbon sources (amylose, CM-cellulose, and pectin), utilizable nitrogen sources (yeast extract and polypepton), and water potential (−1.7 Mpa).