Tokyo metropolitan police said the man turned himself in to Fukui prefectural police in western Japan.
The small drone found on Wednesday had traces of radiation and triggered fear of potential terrorist attacks using unmanned aerial devices.
No one was injured and Prime Minister Shinzo Abe was traveling at the time.
Police have not determined whether the man was responsible for the drone or had broken any law. He hasn't been arrested, and his identity has not been released.
Fukui is home to about a quarter of Japan's 48 workable reactors, which are currently all offline following the 2011 Fukushima disaster. Abe's administration wants to restart as many of the idled plants as possible.
The drone was carrying a small camera and a plastic bottle containing what police suspect was the source of radioactive cesium, levels of which were too low to affect humans or the environment.
The government has set up a taskforce to compile a legal framework for the use of small drones and ensure the security of key government facilities.
In the United States in January, a drone flown by an off-duty intelligence employee crashed on the White House grounds.
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