Trace U was released from the Fukushima Daiichi Nuclear Power Plant (FDNPP) during the meltdowns, but the speciation of the released components of the nuclear fuel remains unknown. We report, for the first time, the atomic-scale characteristics of nanofragments of the nuclear fuels that were released from the FDNPP into the environment. Nanofragments of an intrinsic U-phase were discovered to be closely associated with radioactive cesium-rich microparticles (CsMPs) in paddy soils collected ∼4 km from the FDNPP. The nanoscale fuel fragments were either encapsulated by or attached to CsMPs and occurred in two different forms: (i) UO2+X nanocrystals of ∼70 nm size, which are embedded into magnetite associated with Tc and Mo on the surface and (ii) Isometric (U,Zr)O2+X nanocrystals of ∼200 nm size, with the U/(U+Zr) molar ratio ranging from 0.14 to 0.91, with intrinsic pores (∼6 nm), indicating the entrapment of vapors or fission-product gases during crystallization. These results document the heterogeneous physical and chemical properties of debris at the nanoscale, which is a mixture of melted fuel and reactor materials, reflecting the complex thermal processes within the FDNPP reactor during meltdown. Still CsMPs are an important medium for the transport of debris fragments into the environment in a respirable form.