The drone was about 50 centimeters ( about 19.7 inches) in size with four propellers and a camera. It carried the radioactive symbol and a small bottle with an unidentified liquid inside, according to local media reports.
Police detected the presence of Cesium 134 and 137, both isotopes found after the Fukushima nuclear accident, at a level of around 1 microSievert. That's about 20 times the background level but far below what would be considered harmful to humans.
Earlier in the morning, a court rejected a plea by residents to halt the restart of a nuclear power station in western Japan. All of Japan's nuclear power stations have been offline since the Fukushima accident in March 2011, but power companies are requesting permission to restart their reactors if they can be found to be resistant to all expected earthquakes.
Some are making a link between the drone and the court decision, but who is being the drone is not yet clear.
Images from TV news helicopters initially showed the drone covered with a piece of cardboard while police gathered. It was later covered by a larger blue sheet as about 50 investigators crowded around the area before it was eventually removed.
Prime Minister Shinzo Abe was away at the time, attending a regional conference in Indonesia.
Japan has no regulations regarding flight of drones up to 250 meters (just over 800 feet), but that is expected to change after this incident.
In January, a small drone was found crashed onto the lawn of the White House in Washington, D.C.
That turned out to be the result of a drunken late night flight by an unidentified worker for a government intelligence agency. No charges were filed in that case.
Martyn Williams covers mobile telecoms, Silicon Valley and general technology breaking news for The IDG News Service. Follow Martyn on Twitter at @martyn_williams. Martyn's e-mail address is martyn_williams@idg.com