You have nudity on television in Japan, this is not a big deal & it is not by any means a staple of Japanese television, just like you have nudity on many television stations all throughout the world with the exception of the United States.
I don't care about that, so as an asside, let's not say that the United States is some sort of puritanical theocracy because there isn't nudity on broadcast tv.
Anyways. Censorship in Japan, of the kind that you are probably being refered to is probably the matrix censorship that they commonly use (by law) for censoring the genital areas of perfomers in Japanese adult video, or AV.
(Edit: As well as with all printed material). I've been told that this law originated along with those instilled by the occupying forces after WWII, but I don't have any reference to this, and I don't know if this is exactly true or completely false...
Regardless, Japan has had a long history of these types of materials being published in different forms, going all the way back to the
Edo period. Japan has a completely different set of mores or moral codes concerning pornography and sex.
To say that Japan is in some way prudent in its action to censor pornographic materials misses the fact that by and large the subject matter of
some of these types of materials
can be of the most risque (and to some people) the most down right bizzare documentation of paraphilia which you will ever see...
...but, to each their own. Hope this helps some.