If you're self-motivated you can get exercise on your own without spending any money. Radio Taiso is still kind of a thing. Really, any stretching or calisthenics routine you can do regularly will be beneficial, whether it's yoga, pilates, body-weight or resistance band training, or martial arts routines like tai chi or qigong. I do a mix of those things when I can.
If you're talking about something costs money... there are regular gyms with weight equipment, climbing gyms, yoga and pilates studios, dance lessons... hmm batting cages if you'd count that... and probably some organized sports leagues too, of all kinds. Of course there's martial arts too, but the amount of physical exertion/exercise involved will vary from class to class. How hard you push yourself is much more important.
Somewhere in between are things like running, hiking and biking, which you can do on your own with the proper motivation and equipment; likewise there are online groups and meet-ups based around these activities to provide motivation and a sense of community to otherwise solo activities.
I concur with @nice gaijin, there is no need to sign up for a gym to work out, although public/municipal gyms are quite cheap (~ 400 JPY per day or half-day, I forgot). Lots of parks offer rudimentary exercise and training facilities which are quite popular with the more senior citizens.