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Internal organs of discarded scallops are rich in omega-3 polyunsaturated fatty acids, but it is not used as a food ingredient due to the presence of toxic substances. Recently, our research team prepared high-quality scallop oil (SCO) from the internal organs of the Japanese giant scallop (Patinopecten yessoensis), in which cadmium and diarrhetic shellfish toxin are below regulated levels. In this study, SCO was prepared from the internal organs of scallops obtained from Mutsu and Uchiura bays in Japan, and was referred to as SCO-M (scallop oil from Mutsu bay) and SCO-U (scallop oil from Uchiura bay), respectively. Acute and subacute toxicity studies were performed to assess the safety of the prepared SCO. In acute toxicity study, mice were orally administered SCO-M and SCO-U at a single dose of 5,000 mg/kg body weight. In a 28-day repeated oral dose toxicity study, the mice were fed diets containing 1% and 5% SCO-M and SCO-U; and in a 13-week repeated oral dose toxicity study, the mice were fed 5% SCO-M and SCO-U. There were no toxicologically significant changes in clinical signs, hematology, blood chemistry, and organ weights at any dose during the experiment. Therefore, it was concluded that SCO-M and SCO-U are safe for use as food ingredients under the experimental conditions of this study.