Last month the MLIT released a list of 58 railway road crossings which were top candidates for improvement (or elimination via grade separation). Keio Railway led the list with 25 railway crossings that posed safety risks and/or congestion choke points. Second on the list was JR Kyushu, with 6 locations. Third was JR Tokai, with 5 locations. The remaining railways had three or less candidate locations. It must be noted that the Keio Railway crossings in question will be eliminated with the completion of the (currently under construction) elevation of the Keio Main Line between Sasazuka and Sengawa (7.2km).
http://toyokeizai.net/articles/-/118244
Actual list of those crossings, from the MLIT:
http://www.mlit.go.jp/common/001126608.pdf