I was spoiled by the American way of obtaining a fishing license. You simply navigate to the Fish and Game website for whatever state you want to fish in and in a short time you can legally fish. This does not appear to be the case in Japan. The laws are very cryptic and in fact one river can be “owned” by several private stocking authorities. For each section of the river you need to buy a separate license. Of course if you do not have a high school equivalency in Japanese you won’t know this… Until you’re getting arrested, worst case scenario, or at the very least you are being chased off by an angry local.
As far as I can tell only the fishing farms, where a private entity stocks a section of river, require a license. If you are fishing small hard to access streams and are practicing a catch and release ethic I don’t think you’ll get in trouble if you don’t have a fishing license. I cannot corroborate this assumption though with any evidence. I have read various websites on fishing certain rivers that claim you have to purchase a license but then provide no information stating where you get said license. Finding information online about fishing in Japan is challenging. If you are supposed to have a license often times you can buy them on the spot when asked by a volunteer with the fishing cooperative.