I’m guessing that most people, who have opportunity to visit Japan, mostly use public transportation. Or are ferried about by a local friends.
But should you rent a car and drive yourself around. This video uploaded two days ago, by JAF, Japan Automobile Federation, might provide useful information.
止まれ [tomare, stop] However, it seems you are required to stop at some intersections that have no signs at all.
Drive safe to enjoy your stay in Japan（English）
Including this one from a year ago.
That is a bit like going to the Netherlands, where bicycle riders are darting about everywhere, and local custom dictates you give way or risk being having a collision and hearing Dutch curse words.
Risk Prediction Training, Urban areas Vol.1