On February 17, 1996, an earthquake occurred northeast of Biak Island, Indonesia, and caused a tsunami. Interestingly, the southwest side of Biak Island, which was not facing the epicenter, had a higher tsunami runup than the facing side. In previous studies, it was assumed that the earthquake triggered submarine landslides. However, as no one has addressed this phenomenon, this remains an unsolved hypothesis. The tsunami arrival times obtained from local people’s testimonies were used to perform backward tsunami raytracing. Considering the raytracing results and multibeam topography, we found four submarine landslide candidates: three submarine landslides and one submarine landslide were located to the southwest and south of Biak Island, respectively. The results showed that the submarine landslide located at 135.624°E and 1.009°S with a length of 950 m, a width of 5000 m, and a thickness of about 75 m seems to explain the observed runup and arrival time. In previous studies, the fault parameters were determined without considering a submarine landslide event. As a result, the models could not explain the observed runup in the southwest coastal area of Biak Island. To tackle this problem, we propose an approach that combines a submarine landslide model and a modification of a previously proposed fault model. Our model explains the observed runup heights well; we obtained a geometric mean of 1.00 and a geometric standard deviation of 1.44.