Use of ground-penetrating radar (GPR) can non-destructively estimate diameter and distribution of coarse roots in Cryptomeria japonica in weathered granite soils under field conditions. Ground-penetrating radar (GPR) has been used as an assessment tool for non-destructive detection of tree root biomass, but few studies have estimated root diameter under forest field conditions. The aim of this study was to clarify whether coarse root diameter of C. japonica in weathered granite soils can be estimated using GPR in a forest. Roots of mature C. japonica were scanned using a 900 MHz GPR antenna before being excavated. The diameter and distribution of excavated roots were compared with those identified by GPR, and the relationships between the diameter and waveform indices in radar profiles were also examined. The detection frequency of the number of roots larger than 5 mm in diameter was 47.7%. Limiting factors affecting root detection using GPR in forest field conditions were small root diameter, increasing root depth, and number of adjacent roots. Only one waveform index, using the sum of time intervals between zero crossings (ΣT, ns) of all reflection waveforms of GPR within the range from the first break time at the root top to the delay point time at the root bottom, had a significant relationship with excavated root diameters. A linear regression model was constructed to estimate root diameter using ΣT, and a significant positive relationship in diameter between GPR-estimated and excavated roots was confirmed. The results in this study indicate that the diameter and distribution of C. japonica coarse roots under forest field conditions could be estimated using GPR and this technique could contribute to future evaluation of slope stability by evaluating tree roots under vulnerable soils, such as weathered granite.