Japan... as far as I know, you must notify and clear in each port you enter. Any local Japanese consulate will have the info you're looking for, or just call one of the information centers here:
Immigration Bureau of Japan Website
What I do know about Japan is that other than a handful of ports on the Pacific side (Nagoya, Yokohama), a couple places in Kyushu, though there are literally hundreds of small harbors, most all are set up for commercial fishing. I lived in Japan for years and thought about importing a Moore 24 or the like and cruising the Sea of Japan in the summer months. Very little wind that time of year though, and hot as well. A short'ish draft and small boat easily driven would have let me into some of my favorite villages. One thing I can say for certain is that I wouldn't want to sail anywhere around Japan after dark. The number of fishing vessels, semi permanent net structures, coastal traffic, etc... is truly amazing. Winter storms on the Sea of Japan are something to behold... huge Siberian low pressure systems move across the relatively shallow waters, pick up moisture and energy, and just rage when they hit the coast. Great for surfing, scary for being in any sort of boat.