Stomach contents analysis showed that the three whale species are highly dependent on small pelagic fish, i.e. Japanese anchovy, Pacific saury and mackerels in addition to copepods and euphausiids. Pianka's niche overlap index showed high diet overlap among whale species that occur in some areas where they feed on pelagic fish. Canonical correspondence analysis (CCA) indicated environmental and biological factors significantly contribute to the diet composition of whales. CCA also explained the distribution patterns of whales in relation to SST, chlorophyll a concentration and geographical variation. These analyses demonstrated that the diet composition of the baleen whales is determined by spatio-temporal environmental factors and the amount of small pelagic fish carried by the Kuroshio Current. The total seasonal prey consumption by whales in the study area was estimated to be 774 000 t of Japanese anchovy (16% of the consumed biomass), 44 000 t of Pacific saury (1% of the consumed biomass), and 140 000 t of mackerels (14% of the consumed biomass), indicating these baleen whales are important components in the ecosystem, and warrant inclusion in fisheries assessments.