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.
A drone marked with a radioactive sign was found on the roof of Japanese Prime Minister Shinzo Abe’s office on Wednesday. The radiation was so low it was not harmful to humans.
Yamamoto said he put radioactive sand in a container on the drone that he got from Fukushima, media reported.
A Japanese court on Wednesday approved the restart of a nuclear power station in the southwest of the country, rejecting worries about nuclear safety in the wake of the 2011 Fukushima radiation disaster.
An earthquake and tsunami triggered meltdowns at a nuclear power plant in Fukushima in the worst nuclear crisis since Chernobyl 25 years earlier- Reuters