In recent decades, conflict between Kuril harbor seals (Phoca vitulina stejnegeri) and local fisheries have become a serious problem in Hokkaido, northern Japan. Catch damage in large-scale salmon set nets may be mitigated by attaching a rope grid to set net funnels. We investigated the effectiveness of different rope grids on catch damage caused by seals, and evaluated hidden impacts on catch caused by the seals using an underwater camera for observation of seal and salmon behavior coupled with on-board observations of catch and catch damage. The rate of seal prevention was highest for rope grid with 20 cm × 20 cm spacing (97.5 %). The percentage of catch damage in the set net with this rope grid was significantly lower than that for the set net with other rope grid which was easy to enter for seals. We concluded that it is effective to attach an appropriate rope grid to set nets to prevent seals from entering fish bags and to ensure salmon catch amounts. The existence of “hidden damage” was quantitatively revealed via the underwater observation of seals removing salmon from the fish bag, and by comparing the number of salmon between underwater observation and on-board observation.