As someone sensitive to the situation jib71 (kind of) describes - where a passenger with an assigned seat may go elsewhere (perhaps the unreserved carriage) rather than risk confrontation by pointing out that there is a child in his/her seat that doesn’t belong there - my personal way to deal with this was to have my child in my lap whenever the train would reach a station and for a few minutes after pulling out. Only once it was clear that an unoccupied seat was going to remain unused could LapInfant go there. When we got to the next station, she’d come back to my lap, and so on, and so on. This was a habit for us, whether in reserved or non-reserved seats, but particularly in reserved seat carriages.

Worth remembering the distaste Japanese people feel for shoes on seats. I recommend shoes that you can take off and put on easily so that the little one can clamber around up there without upsetting anyone. As a parent you can spend a HUGE proportion of a journey putting shoes on and taking them off as walking on the floor in socks or pram shoes is not appreciated either. Socks/bare feet for the seats, shoes for the floor.
Same thing for any play areas you might come across - if you see barefoot kids in a delineated area or on carpet your child can join them, just make sure the shoes come off first - and same for you if you need to go in and get your kid out.