Well if you can get the Monbukagakusho scholarship (which you can see has been pretty heavily discussed on this board), then it won't cost anything to get your master's degree at one of those schools.
In order to get a master's you must take some courses, and chances are that those courses will only be offered in Japanese, so you should work on that either way.
If your English is good enough to communicate and your professor also speaks English, it's possible that your research activities can mainly be done in English.
By the way, for a number of reasons, I think it can be a bit harder to get into a Japanese university without going the Monbukagakusho scholarship route, so I would encourage you to look into that. Also, work on both your English and Japanese; in order to get the scholarship you must display a certain level of proficiency in one or the other.
Hope that helps!