I imagine that you didn't select your university yourself. (it would have been incredibly stupid to choose a university and supervisor in a university where you don't have the sources or equipment for research)
This probably means that MEXT had to look for a university for you. You can be happy that they found you a university where you can start to study Japanese and prepare for your master's course. However, I think that it is a good idea to apply for the master's course at a university better suited for you. This will also include passing the entrance exams (for the master's course) from the other university. I would suggest you don't wait too long (as soon as your Japanese gets decent you can start) to look for that and that you try to find contact with professors from the other university you want to apply to.