The influence of sympatric large animals on the sleeping behavior of primates in the wild is still largely unknown. In this study, we observed behaviors of wild Japanese macaques (Macaca fuscata yakui) at their sleeping sites, using a highly sensitive video camera. We found evidence of nocturnal interspecific interactions, such as agonistic interactions, between Japanese macaques and sika deer (Cervus nippon yakushimae). Deer approached sleeping clusters of macaques, which slept on the ground, to eat their feces or unidentified materials near the sleeping clusters, and as a result, the macaques were often quickly displaced from their sleeping site. There was a significant difference in the occurrence of macaque–deer agonistic interactions between seasons. Our results suggested that the size of the sleeping cluster, the number of adult macaques in the cluster, and the existence of adult males in the cluster did not influence the occurrence of the agonistic interactions. Finally, we discuss the influence of this interaction on macaques and speculate on the influential factors leading to nocturnal coprophagy of macaques’ feces by deer.