Camping "wild" is very common, even in an urban area. Just be discrete and stay out of sight, and don't set up your tent till after it gets dark, or starts to. If hassled, it's easy to say that you were trying for a campground but got lost, had a flat, ran out of time/daylight, etc.
Try posting your question on a cycling forum such as Japan Cycling Navigator, or Tokyo Cycling Club.
on edit:
http : // www . japancycling . org / v2 / info / camping . shtml
(remove the spaces)