Discarded scallop internal organs, especially the hepatopancreas, are rich in n-3 polyunsaturated fatty acids such as eicosapentaenoic acid and docosahexaenoic acid. However, they have not been utilized because of their contamination with toxic substances, such as cadmium (Cd), and the occurrence of diarrheic shellfish toxins (DST). We have successfully prepared a high-quality scallop oil (SCO) from the internal organs of the Japanese giant scallop (Patinopecten yessoensis), including the hepatopancreas without Cd and DST. These pollutants were removed by liquid-liquid partitioning followed by adsorption to active carbon of fine particle size with high pore surface volume. In this study, we prepared SCO from scallop internal organs obtained from two different processing areas (Mutsu and Uchiura bays, Japan), and referred to them as SCO-M and SCO-U, respectively. Genotoxicity of SCO-M and SCO-U was evaluated by the in vitro bacterial reverse mutation test (Ames test) and in vivo micronucleus test in accordance with the Organisation for Economic Co-operation and Development guidelines. SCO-M and SCO-U showed negative results in the Ames test in the presence or absence of metabolic activation with S9 mix. In addition, no genotoxic effects of SCO-M and SCO-U were observed at all tested doses in the micronucleus test. Based on the results of the present study, it can be concluded that SCO-M and SCO-U are safe products in terms of genotoxicity under these experimental conditions.