Bob
I don't think you have a choice there. In my country, there's only the option for research studies students and if you want a masters degree, you have to apply for an extension of your scholarship to MEXT while you are in Japan. I know of an alumnus who stayed there for four years: two for research and other two for masters. I think this applies everywhere.
For me, I'm in my first year of campus but considering the time constraints should I go for research, I decided to apply for undergrad and forfeit that one year. After all, I don't know Japanese and it might take longer.
Hope that helps.
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