First the bad news: Japan is extremely hilly and all these hills are forested, so finding a flat spot can be a big problem. And if there is any flat ground it is either completely built up or used as farmland. Now the good news: Apparantly there is no law against free camping in Japan and the Japanese are very tolerant, so here you can camp in places you would not even consider in Europe.
So all in all we had mostly very good camping experiences: We either manage to find a flat spot in a forest or next to a river or we ask people for permission to camp on their land. Despite my Japanese language course I am not exactly fluent in Japanese, so I have a little piece of paper in Japanese for that purpose. And if you manage to find someone who can read it without glasses you usually get very positive reactions. We were offered to stay in a garage (which we refused) and invited into a house (which we accepted), but usually people try to direct you to a suitable place.
One day we had to camp next to some greenhouses hiding behind haystacks. There was no one around to ask for permision so we just pitched the tent. To my great horror the farmer showed up in the morning before we had left and I expected the very worst... But instead of yelling at us the farmer seemed to be utterly delighted to find 2 smelly foreign cyclists on his property. He could not stop laughing and offered us lettuce and peas out of his green house! Now, that would not have happened in Germany!
Also very handy are picnic and rest areas along roads or tourist spots. They usually have a shelter that comes in very handy when it rains and it rains a lot here! It is very comfortable to sit under a roof and cook and eat while it is pouring down outside and nobody seems to bother when we camp there.
Only once did we run into trouble: We were already late finding a campsite and pitched our tent in a small decrepit park in a residential neighborhood. We had already started to cook dinner when half of the neighborhood showed up to tell us that they did not want us to camp there. They were very friendly, but the definitely wanted to get rid of us. They even showed John a different camp site by car and so we had no other choice than to leave. The new campsite was in a posh park and we would never have chosen that site for camping ourselves. But if the locals recommend it...... they recommended shit, because at 22.30 a security guard showed up and wanted us to leave. How much bad luck can you have in one day? John tried his best sweet talking in sign language and to our big surprise the guard permitted us to stay - but we had to promise to leave before 7 in the morning.