On some occasions its impertinence was tolerated but at other times the deer bolted and ran. The monkey ejaculated on the backs of the does, which licked the seminal fluid, researchers said.
"No ambiguity is possible, it is clearly sexual behaviour," study co-author Marie Pele of the University of Strasbourg, France, told AFP.
Furthermore, the monkey appeared to "guard" the targets of its affection, chasing away other male macaques.
The scientists speculated the behaviour may be driven by "mate deprivation" in a community where competition for females is stiff, boosted by a surge of hormones in the breeding season.
"Sometimes young males, like the one in the study, do not have access to females in their social group as these are claimed by older males," said Pele.
"This young macaque... did not have access to females, but was very excited. It took advantage of the presence of the doe."
Snow monkeys and Sika deer live in close proximity at Yakushima -- the deer eat food the monkeys drop from the trees, and sometimes feed on their faeces.
The team said further study is necessary to understand the origins of interspecies sexual behaviour, including zoophilia -- when humans are sexually attracted to animals.
The only other published scientific study on inter-species sexual behaviour was the much-publicised 2014 report of fur seals forcing themselves on penguins in Antarctica, the authors said.
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