To analyse the 137Cs distribution and migration under various fractions of organic matter layers, this study investigated easily recognizable, originally shaped organic L-fractions, and not easily recognizable, early fermented and fragmented organic F-fractions, of both oak (Quercus serrata) and cedar (Cryptomeria japonica) sampled from Osawa watershed sites at Nihonmatsu City, Fukushima Prefecture, Japan. The organic materials were put on top of soil columns from Field Museum (FM) Tamakyuryo in Hachioji City, Tokyo. The 137Cs vertical distribution in forest soil profiles was analyzed using the relaxation mass depth, ho (kg m−2). Soil columns with both L and F- organic layer fractions of both oak and cedar, labelled as Oak-L, Oak-F, Cedar-L and Cedar-F with four replications (n = 16), were set up by the laboratory column-based method and kept under five months’ incubation period. Soil columns after incubation were sampled at depths of 0–1 cm, 1–2 cm, 2–5 cm and 5–10 cm. Results of 137Cs inventory in the organic fractions showed that 86% (oak and cedar) of the total organic layer fractions 137Cs inventory accumulated within the F-layer, indicating that the transformation of litter is a huge source for potentially mobile 137Cs, especially the oak F-layer (67% 137Cs inventory) and further continuous transfer into the forest soil mineral layers. A higher ho in L treated soils (Oak-L and Cedar-L) compared to the F treatments implied that the low 137Cs amounts penetrated faster and deeper due to their water-soluble nature. Furthermore, Cedar-F showed a higher ho of 24.3 kg m−2 than Oak-F of ho, 14.0 kg m−2, and a significant positive relationship between 137Cs retention and total carbon (TC) (p < 0.05) suggested the influence of soil organic matter on 137Cs penetration and retention. The C/N (carbon nitrogen ratio) results revealed that organic matter fractions of high C/N including 137Cs, as observed in Cedar-F, in which decomposition does not advance, penetrates soil depths while the organic matter fraction of low C/N, observed in Oak-F, showed that decomposition advanced to release 137Cs which was held by adsorption unto the RIP (radiocesium interception potential) of soil surface. In addition, infiltration by water as a transportation process was suggested to largely influence the downward migration and retention of 137Cs at lower depths of Cedar-F.