Chemical stratigraphy is useful for dating deep sea sediments which sometimes lack radiometric or biostratigraphic constraints. Oxic pelagic clay contains Fe-Mn oxyhydroxides that can retain seawater 187Os/188Os values, and its age can be estimated by fitting the isotopic ratios to the seawater 187Os/188Os curve. On the other hand, the stability of Fe-Mn oxyhydroxides is sensitive to redox change, and it is not clear whether the original 187Os/188Os values are always preserved in sediments. However, due to the lack of independent age constraints, the reliability of 187Os/188Os ages of pelagic clay have never been tested. Here we report inconsistency between magnetostratigraphic and 187Os/188Os ages in pelagic clay around Minamitorishima Island. In a ~ 5 m thick interval, previous studies correlated 187Os/188Os data to a brief (< 2 million years) isotopic excursion in the late Eocene. Paleomagnetic measurements revealed at least 12 polarity zones in the interval, indicating a > 3.3–7.4 million years duration. Quartz and feldspars content showed that while the paleomagnetic chronology gives reasonable eolian flux estimates, the 187Os/188Os chronology leads unrealistically high values. These results suggest that the low 187Os/188Os signal has diffused from an original thin layer to the current ~ 5 m interval, causing an underestimate of the deposition duration. The preservation of the polarity patterns indicates that a mechanical mixing such as bioturbation cannot be the main process for the diffusion, so diagenetic re-distribution of Fe-Mn oxyhydroxides and associated Os may be responsible. The paleomagnetic chronology presented here also demands reconsiderations of the timing, accumulation rate, and origins of the high content of rare-earth elements and yttrium in pelagic clay around Minamitorishima Island.