Drones laws in Japan are governed by the amendment to the Aviation Act that came into effect 10 December 2015.
Flying a UAV over a prohibited area or violating the conditions of flight is punishable by a fine of up to
Source: Civil Aviation Bureau
Updated November 2017
I carried my drone (DJI Phantom 3 Professional) to Tokyo, Kyoto, Hakone, Hiroshima but I only flew it over the Katsura River in Arashiyama and Lake Ashi in Hakone. Most of the temples, monuments have no drones allowed signs hanging at their entrances. Not only that, some cities (such as Hiroshima) do not allow drone flights.
Japan’s been slightly paranoid about drones ever since someone flew a drone carrying radioactive sand over the Prime Minister’s office in Tokyo. Since then the laws have gotten stricter and the punishment more severe.
In fact Tokyo Police possesses drone catchers in case you don’t listen to their warnings. So yes, be sure to always adhere to drone laws in Japan.
As drone flights are strictly regulated in most cities, go towards the outskirts. Or find a secluded area with few people, or preferably near a water body (river, lakes, sea).
I think this graphic from the Civil Aviation Bureau of Japan perfectly highlights the dos and don’ts of flying drones in Japan.