Tokyo metropolitan police said the man turned himself in late yesterday in Fukui police in western Japan.
The small drone found on Wednesday had traces of radiation and triggered fears of potential terrorist attacks using unmanned aerial devices, police said.
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Police said Yasuo Yamamoto, 40, is facing charges of flying the drone and obstructing duties at the prime minister's office.
Public broadcaster NHK said police quoted the unemployed man as saying he did it to protest the government's nuclear energy policy.
Fukui is home to about a quarter of Japan's 48 workable reactors, which are currently all offline following the 2011 tsunami-triggered Fukushima plant 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 suspect said he used the sand from an unspecified location in Fukushima, where radiation levels are still high due to fallouts from the Fukushima Dai-ichi meltdowns, NHK said.
The government has set up a taskforce to work on regulations for the use of small drones while ensuring the security of key government facilities.
It is not clear exactly when the drone landed because workers at the office in central Tokyo rarely go up to the roof. An official taking new employees on a building tour reportedly spotted the drone.
In the US in January, a drone flown by an off-duty intelligence employee crashed on the White House grounds.
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