The Fukushima Daiichi nuclear power plant accident resulted in extensive radioactive contamination of the surrounding forests. In this study, we analyzed fallout 137Cs, 134Cs, and 131I in rainwater, throughfall, and stemflow in coniferous forest plantations immediately after the accident. We show selective fractionation of the deposited radionuclides by the forest canopy and contrasting transfer of radiocesium and 131I from the canopy to the forest floor in association with precipitation. More than 60% of the total deposited radiocesium remained in the canopy after 5 month of the initial fallout, while marked penetration of the initially deposited 131I through the canopy was observed. The half-lives of137Cs absorbed in the cypress and cedar canopies were calculated as 620 days and 890 days, respectively for the period of 0–160 days. The transfer of the deposited radiocesium from the canopy to the forest floor was slow compared with that of the spruce forest affected by fallout from the Chernobyl nuclear reactor accident.