Don't go Nude!
In Japan, the concept of nude tanning at beaches does not exist. They call this mittomo nai, or unsightly. It is acceptable to go shirtless or wear a bikini.
At the same time, if you go to a remote beach, then there is nothing to worry about. But definitely don't go nude at a major public beach.
In most Japanese bath houses, it is acceptable to go nude. If that makes you uncomfortable, make sure to confirm whether the bath house allows nudity or requires participants to wear a swimsuit. Most coed bath houses require a swimsuit.