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Since I just got finished finding a flat, here are some of my answers:

Is it hard to find a flat or a house for rent in Tokyo?
VERY hard if your looking for short term accommodations (under 3-6 months), if you are staying longer you will have a lot of choice but obviously with long term stays there are a lot of fees that go along with renting like key money and other such thing.

How to find a home in Tokyo: classifieds, real estate portals, real estate agencies?
Google was the best, almost every site I was recommended was within the first 3 pages of my Google searches, you just have to know what keywords to search. I did well with 'Apartments in Tokyo', 'No key money apartments in tokyo', and for my purposes: 'short term apartments in tokyo'.

How much is the rental for a house, an apartment?
This I found was definitely determined by how close you are to the rail lines and downtown Tokyo. I ended up with an apartment close to Ueno which is $850/week. If I took the offer of an entire 3 bedroom house just south-west of Tokyo (25-30min train ride into tokyo) I would have paid only $500/week. So really its like any major city, if you are willing to take a hit on travel time then you can get more bang for your buck. I just wanted to be central to the places I need to go, so I am within walking distance of the places I need to be while I am there..and obviously I am paying for it.

What are the formalities or the required documents for renting an accommodation?
Unfortunately I dont know much about this, for short term rentals I just paid a deposit via paypal and filled out a rental form with my information, flight info and agreed to some terms.

Hi jamilv!

Thanks for your contribution

Armand