Harago, an assistant professor at Japan's Meiji Gakuin University and a specialist on deforestation, arrived in Istanbul on Wednesday, police told AFP.
A hotel employee found his body Thursday, wedged in a narrow airshaft at the hotel in Istanbul's European district, the source said, adding that it was not yet clear whether the death would be treated as an accident, a homicide or a suicide.
The Japanese consulate in Istanbul would not comment on the death of Harago, 47, who was active in several environmentalist groups, including the Japan-Brazil Network.
He was the author of several articles and books on tropical forests and deforestation problems.