The elephant, a 40-year-old, 3.5 ton female, flung her Thai mahout (elephant handler) Wichai Madee against an iron fence while he and another handler were washing her. She then pushed his body around the enclosure with her trunk.
Madee was rushed to the hospital, the Bangkok Post reports, but he was pronounced dead within an hour.
The incident occurred in the morning, before the Adventure World complex in western Japan opened.
Elephants, though they can appear docile in captivity, are among the world's most dangerous animals, killing about 500 people per year, according to a number of sources.
Mahout deaths in Southeast Asia, where elephant tourism generates income for many rural communities, are common. A report by the Atlantic last year found that at least four mahouts in Thailand had been killed by their elephants in March 2016 alone. That story was sparked by an incident in which an elephant killed its handler and ran off with a family of tourists on its back, but events like that are not unique.