No injuries or damage have been reported from Wednesday`s incident, and Prime Minister Shinzo Abe was away on a visit to Indonesia to attend the Asia-African conference.
Police said Wednesday it was not immediately known who was responsible. They are investigating the possibility it had crashed during a flight.
Public television NHK footages showed dozens of police and officials around the drone, which was covered by a blue tarp.
NHK said the drone is about 50 centimeters (1.7 feet) in diameter and had four propellers, carrying a small camera and something that looked like a flare. It was also decorated with a symbol that warns of radioactive material.
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