Unemployed Yasuo Yamamoto, 40, who lives in Fukui Prefecture in western Japan, was arrested on Friday and charged with obstruction of official business, police said.
The maximum penalty is three years in prison or a 500,000 yen [$4,200] fine.
Media reported that Yamamoto turned himself in at a police station in Fukui and said he landed the drone as a protest against nuclear power.
Police in Tokyo and Fukui declined to comment on Yamamoto's motives, saying the investigation had not finished.