I know that the living cost there is between 120k-200k JPY
You
know this?
Really?!?!?!? Who ever said that? A mere 120K is essentially living in a cardboard box in most bigger cities here, and to say this is for Tokyo is just ludicrous. Please state your source for this outlandish claim, especially the lower figure.
If I were to presume, may be I will be able to make at least 50k JPY of savings per month, but I'm also concerned with accidental expenditures, such as doctor visit and medicines.
You've been give wise advice so far about these things, and you definitely need to be concerned, even being paid 200k.
You'd need to find very, very cheap housing and certainly not anywhere near downtown. It would likely be a 6-tatami 1-room place, perhaps even with shared toilet/shower. See how
tiny it is!
All residents are required to sign up for the national health insurance. National health insurance is not free - everyone pays into the system.
The first year you will probably pay only 2,500 yen/month, but please confirm this with your school or ward office. The year after that, they know how much you are making, even in scholarships, so the amount goes up approximately tenfold as a standard fee. (Don't listen to anyone who tells you, "Hey! Not everyone pays! I skipped out, and I know some Japanese do!" Those skinflints are running a big risk, and that is to have to make backpayments up to 2 years' worth if they are ever caught.
Well, I am considering to do my PhD in Tokyo and that 200.000 JPY per month is the expected scholarship. If I'm accepted I will choose to live in a student dorm with typical monthly fee of 40k-70k JPY.
So, why are you asking questions about housing? (at least, it seems that you are)
Monthly expenses are things I have calculated and doled out to people for almost 20 years now. Food costs vary considerably because we don't know what you are satisfied eating, and whether you are a carnivore, vegetarian, or vegan, and whether you are able/willing to cook for yourself in a manner that actually saves money. You know your dorm costs (ask about utilities for water and electricity, which will vary with personal preferences and the season). If you get a scooter, ask about its insurance and fees for parking. Used bikes are cheap and handy, and if you live on campus, a grocery store shouldn't be that far away. Want a phone? You'll pay 10,000 for installing service on a cell phone, plus 5,000-8,000 yen/month thereafter. Installing a landline phone is far more expensive. Ask what options you have to get Internet in your dorm room; you might just want to go with an Internet cafe or use computers on campus instead (and your cell phone). You are smart to consider emergencies and such. The unexpected does come up. Have you factored in any sort of costs for dry cleaning, gifts, souvenirs, postage, hair care, and regular dental visits? My calculations for people have been based on 250,000 yen/month and paying roughly 70,000 in rent, and they allow people to save 50,000 yen/month but only if they are relatively frugal. You don't have to pinch pennies, but you need to know how to cut corners a little. Since you're expecting only 200k, you'll have to pinch a little more.