you need to do more of your own research--especially because Americans generally are not familiar with the Japanese university system. You can Google everything nowadays. By simply going to the University of Tokyo webpage (which, remarkably, is by default in English), and clicking on a tab that says "Degree Programs in English", one can find this:
http://dir.u-tokyo.ac.jp/ICE/course/course10.html
http://www.chem.s.u-tokyo.ac.jp/en/academic/
http://www.chem.s.u-tokyo.ac.jp/en/academic/ir-student.html
http://www.chem.s.u-tokyo.ac.jp/en/academic/doctor.html
So English-language postgraduate degrees are available in chemistry at Tokyo. You should look up to see if courses are taught in English or Japanese though. Also consider, of course, that even though a course is taught in English, the English might not necessarily be fluent. Note that the East Asian methods of teaching are entirely different from those of the West. Much more discipline, focus, and book-studying is required.
Most younger middle/upper class East Asians can speak some English. However, you obviously would need to learn to read and speak Japanese to a certain degree of fluency to survive in Japan for a long term academic stay. The university will have more English fluency, but Tokyo itself still has most of its signs, etc. in Japanese. And Japanese civilian English is not known to be all that great.
So if you really are set on doing a graduate degree in Japan, I would sit down for a good few hours and search around the Internet. As I just demonstrated above, you can pretty much just go to the university website, browse a bit, and land on the information you want.