Anguillid eels generally exhibit catadromous migration between oceanic spawning grounds and freshwater growth habitats, but some individuals remain in coastal or estuarine saline waters for growth. This migratory plasticity had been considered to be a conditional strategy based on individual energetic status during the glass eel stage. Several studies have examined whether salinity-based habitat selection is linked to individual body conditions, but while frozen specimens of European eels showed this relationship, anesthetized samples of American eels did not. Here, we report that freezing preservation under different salinity levels influences body-condition evaluation in Japanese eels. Behavioral tests of Japanese eels did not reveal significant differences in anesthetized body conditions between those choosing saltwater and those choosing freshwater. In conclusion, the body conditions of glass-eel-stage Japanese eels are unlikely to be associated with their salinity-choice propensity.