Japanese agriculture uses large amounts of plastics. Fertilizer-containing plastic microcapsules with a diameter of 2–5 mm (“coated fertilizer”) are not recovered after use, and after diffusion of the fertilizer components these microcapsules are found in large quantities, not only on agricultural land but also along the coast of Japan. Here, we investigated the accumulation of microcapsules derived from coated fertilizer in 19 paddy fields. Microcapsules were detected in all of the paddy fields surveyed, at concentrations in the range of 6–369 mg/kg (mean 144 mg/kg)—much higher than the concentrations of microplastics in farmlands in other countries. There was no difference in mean microcapsule concentration between sampling sites with continuous rice cultivation and those with crop rotation, but that of a paddy field that had never received coated fertilizer was significantly lower. Examination of the spatial distribution of microcapsules in one paddy field showed that there was a hot spot with a high concentration near the drainage outlet. This was likely due to the strong influence of irrigation water flowing from the water inlet to the drainage outlet. The amount of microcapsules accumulated in Japanese paddy fields, as estimated from our results, and the amount applied to the fields, as estimated from the statistics, were almost equivalent. Therefore, most of the microcapsules that have already been applied to paddy fields may continue to accumulate. The impact of these high concentrations of microcapsules on the soil environment needs to be assessed.