Hey
Which level of scholarship are you asking about? Undergraduate or masters?
If it's undergrad, For the first year at the language institutions, you'll stay at the dorms for international students where you'll pay your rent from the allowance they give you. I'm not sure if that's the case when you join university, but you can also look for your own apartment if you wish which of course requires higher rents.
Mext is there to take care of your needs, both academic and also your lifestyle. I don't see why you should worry much. You'll have mentors on your first day of arrival and at least you won't feel so lost. Well that's what I've learned from previous mext scholars on the internet.
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