Drone laws in Japan have become strict. There was one idiot flying onto the prime ministers office and landing there with radioactive material.
(see:
Drone 'containing radiation' lands on roof of Japanese PM's office).
After this incident it did not take long before the laws on drones were made a lot stricter. Generally speaking there is no flying allowed in the city limits, above roads, parks or any populated areas. Fines are high if you get caught (around 5,000$) so I would not recommend still doing so. They could also lock you up without further questioning and ban you from the country afterwards. Unlikely, but possible.
Now on to the positive parts: If you go out to Nagano and only fly around not too populated areas, untouched nature etc. you should not have a problem. I also recommend getting up REALLY early if you don't want to encounter people. I got up around 4.00 am on some days just to make sure I am the first person on location and would not have problems with crowds. Of course there where bystanders at times, but I never had problems. They watched, where amazed, waved at my drone but nobody had a serious problem.
Airports: Keep the drone in your carry on. I flew around a lot and came trough several airports. They checked it throughly every time, especially the batteries. But I was always free to go. A little Japanese here goes a long way here, but is not necessary. I have friends who had their drone in there checked in luggage und they mysteriously broke on the way. 2 friends, same flight, 2 broken phantoms. It was a flight to Spain and my guess is the personal at the airport broke it because some people view drones as an annoyance on their beaches and tourist spots.
Here is a link on the current laws in Japan:
Current Law on Drones and UAV's in Japan
So to wrap things up all I can say is: If you play by the rules you should not have any problems, so happy flying!
And be sure to share the videos here, can't get enough of Japan and am already planning my next trip.