The increase in the frequency of occurrence of abnormal weather could include severe rainfall, which could cause rice submergence during the ripening stage. This experiment was conducted to clarify the effects of submergence during the ripening period on yield and quality of rice. The flooding treatment was conducted at 7 and 14 days after heading. Flooding conditions were created with two conditions, flag leaf exposed and overhead flooding, and each condition was divided into two conditions according to water quality—clear and muddy. Although the yield decrease was more severe at 7 days after heading because of the decrease in the ripening ratio, the head rice ratio was more affected at 14 days after heading because of the increase in the chalky kernel ratio. The maximum quantum yield (Fv/Fm), which indicates the photosynthetic efficiency, did not differ before and after the flooding treatment until flooding continued for 4 days. In addition, stem elongation occurred because of flooding as an avoidance mechanism in japonica rice. This phenomenon was expected to decrease the supply of assimilation products to the spikelet (sink). Overall, it was suggested that additional experiments should be conducted examining the change in the starch synthesis mechanism and transfer of assimilate products resulting from submergence, for development of cultivation techniques corresponding to submergence and breeding of varieties with submergence tolerance characteristics.