Catches of whitebait, sardine fry, sometimes contains other marine animals, including fishes, mollusks, and crustaceans, and therefore boiled and dried whitebait products may contain these marine animals if sorting is incomplete. In September 2014, contamination of boiled and dried whitebait products with pufferfish juveniles became a serious food safety concern, as tiger pufferfish Takifugu rubripes juveniles are toxic and contain tetrodotoxin (TTX). The toxicity of the juveniles of other pufferfish species, however, is unclear. To evaluate the food safety of whitebait products contaminated with pufferfish juveniles, we identified the species and toxicity of pufferfish juveniles contaminating whitebait products processed between July and September, 2014. Nucleotide sequence analysis of 16S rRNA or cytochrome b gene fragments of the mitochondrial DNA indicated that partial sequences of the polymerase chain reaction products of 15 specimens were identical with those of Lagocephalus spadiceus, and partial sequence from 2 specimens were identical with those of Takifugu vermicularis. We analyzed TTX by liquid chromatography-tandem mass spectrometry. TTX was not detected in the L. spadiceus specimens and was below the quantification limits (30 ng/g) in a T. vermicularis specimen. Based on whitebait product manufacturer's research, 795 individuals and 27.2 g of pufferfish juveniles were detected in 8,245 kg whitebait product. Thus, the ratio of pufferfish to whitebait product was estimated to be 0.096 individual/kg whitebait product and 0.0033 g/kg whitebait product, respectively.