One of the things I really like in Japan is the ease to take photos of the people around. From my experience, it’s extremely rare for the Japanese people to refuse being taken. They will even thank the photographer! This is probably another one of these unique characteristics of the Japanese people.
So, do not be afraid to ask, even only by showing your camera and make the people understand that you’d like to take their photo. It’s often the start of a small conversation or exchange.