Japan: drones are restricted — permits required for most areas.
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Drones in Japan are restricted — permits required for most areas. Flying over populated areas (which covers most of Tokyo and other cities) requires advance permission from Japan's aviation authority — plan well ahead if you want to fly.
Yes — register before you fly, not after you land. Few authorities offer same-day approval, so this needs to happen before your trip.
Unlikely if you've completed the required registration, but keep your registration certificate or permit accessible in case customs asks.
Yes — photographing military sites, government buildings, and some infrastructure can be restricted almost anywhere in the world, drone or no drone. When in doubt, don't photograph it.