Luckily Japan currently has some fairly liberal drone laws and most of them boil down to common sense rules like not flying near an airport or not flying over people and crowds or in built up areas and you currently don't need to register or have a license for hobby drones but that may change if folk start doing stupid things. There is a summary in English of the current drone laws here at Drone Law Japan and a fuller guide to the laws here at MLIT in Japanese. To cut a long story short, you shouldn't fly within 9km of an airport and in most areas can't fly over 150 metres in height, you can't fly over large cities without permission and you need to maintain line of sight with the drone at all times (unless you've obtained permission beforehand). You can't fly at night (again without permission) and you shouldn't fly while drunk apparently. The government are looking to liberalise the line of sight rules to allow for inspections of power lines and other infrastructure in remote location but that's probably not going to happen anytime too soon.
Haven't got the hang of making well shot videos yet but using one of the automated flight modes did manage to shoot this video