So yes, as nice gaijin has pointed out, the public baths are divided by sex, but otherwise open--all the guys in the guy's half are washing at the faucets, using the little stools, and then after having washed and rinsed (at least to some degree) everyone enters the same bathtub--but it's a big bathtub and not all enter at the same time, of course.
There are some public shower rooms that you can find at places. These are private, but as far as I know, far and few between.