The early life history traits of Japanese flounder Paralichthys olivaceus, a commercially important species, have been well studied; however, daily ring formation in otoliths (lapilli and sagittae) of this species has not been investigated in detail. We examined the daily periodicity of ring deposition in otoliths using hatchery-reared Japanese flounder larvae and juveniles. In both lapilli and sagittae, a check corresponding to the radius at hatching (ca. 6 µm) was discernible throughout the pelagic larval and settled juvenile periods. The otolith rings were faint in the preflexion larval period and distinct in the flexion larval and later periods. Regression analyses for the number of rings by age in days showed that ring deposition occurred daily in lapilli but not in sagittae. Double marking of juveniles with alizarin complexone confirmed the daily ring periodicity in lapilli. However, the first faint ring was observed in the innermost areas in lapilli at 3–16 d post-hatching, and the faint rings were often unrecognisable, even under a scanning electron microscope, which interfered with daily age estimation. To estimate the number of days corresponding to the obscure zone with unrecognisable rings in lapilli, we developed the estimation method using logarithmic functions derived from the relationship between the radius (restricted to <20 µm) of lapilli and the ring counts for individual data. The error for the estimated days was − 0.05 ± 2.13 (n = 26, mean ± SD), indicating that this method is useful for hatch date estimation. Thus, the present study provides a novel method for analysis of otolith daily increments with unclear narrow rings in the innermost part of the otoliths.