Was Kodomo no Jikan controversial in Japan?
At least for anime version, there are some discussion and some TV station cancelled the series.

From Wikipedia:


  [...] two television stations — TV Saitama and Mie TV — removed it from their broadcast schedules. In an official press release, TV Saitama stated that their decision was heavily influenced by the then-recent capture of Takayuki Hosoda, a notorious Japanese child  pornographer who was revealed to be an elementary school vice principal.


I haven't read Kodomo no Jikan yet. In my understanding, Kodomo no Jikan contains two taboos. One is sexual interest from child, and the other one is love relationship between teacher and student.
First one is also controversial in Japan.
But for second one, it doesn't get any attention in Japan (if it's in fiction).

Other example of teacher-student taboo in US is Cardcaptor Sakura.
This anime was aired by NHK (BBC or PBS equivalent in Japan). It's not controversial in Japan.
But the NA version was heavy edited.
All love relationship between teacher and student was removed with same-sex love relationship.
(e.g. father and mother of protagonist met each other when the mother entered university that the father worked as professor.)