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.
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.