Perhaps the most curious thing I found when searching for accommodation in Japan online, was the difference in prices between Japanese sites and English sites. English sites offering both long or short term stay to foreigners either only offer the premium end of real estate for rent or jack up their prices by A LOT. After looking through some of the listings, I am convinced it is the latter.
Typically in Japan when looking for a new place to live, one would find a real estate agent. Real estate agents are literally everywhere, and if you watch Japanese television you would notice 3 out of 5 commercials are from real estate companies. Unlike the western world, real estate agents receive the majority of their business through renting places, rather than from selling them. Direct negotiations with owners found via platforms like craigslist or other forums are almost non-existent, unless you happen to know the owner.
Enter the real estate agent. The agent will usually present you with a handful of listings that match the criteria you set (location, size, price, etc.). He will then take you out to see the ones you are interested in, and when you are satisfied, you will lock on a contract of no less than a year. On top of that, you pay a real estate agent fee, which is usually equivalent to more or less one month of rent, and in addition pay some 'key money' to the owners of the listing. 'Key money' is another way of taking your money, because they can, as you get no added value in return. If your agreement is to pay rent monthly, you would generally make the payment to either your real estate agent or the property management company via cash or bank transfer.
In Japan, your resident status means everything. For a foreigner, this is shown in the Zairyu card. If you do not have a zairyu card, meaning you do not have a visa, your options for rent become very limited and it is very difficult to rent. Very few real estate agents will work with or have experience working with non-residents and may reject you immediately based on that. There are, however, some options.
Larger real estate companies will generally have some short-term places available. They are not targeted to foreigners specifically, but you have the option to rent them. They are attractive because most come furnished which is uncommon in Japans. Moreover, prices are fairly reasonable. Using this method, you can probably rent a ¥50,000/month place for ¥70,000/month, a¥70,000 place for ¥90,000, etc., which is much better than the ¥150,000/month+ that most English real estate places charge for similar places.
The downside, however, is since you will most likely not be able to get a guarantor to back you, they require a full payment of the entire term up front. In other words, if you were to rent a place at ¥70,000/month for 6 months, you would have to prepay the entirety of ¥420,000 +commission & key money. Also note most local real estate agents won't speak English.
The second option is Leopalace 21. I've never actually used those guys, but they offer short-term rent for foreigners, and are definitely a bit more expensive than renting on your own. They appear to be popular among foreign students. Units are also small, but in terms of convenience this is the way to go.
Certificate of Residence (Jyumin-hyo 住民票) – You are required to report where you reside in Japan to your district office and in return receive a Jyumin-hyo. This document is very easy to get and serves no other purpose than to provide an address for the government of Japan to send you a tax bill every year. (Yes, everyone has to pay extra annual taxes for just being alive in Japan). More importantly, it is one of the documents real estate agents will have you present so make sure you have it.
A guarantor or two – You will generally be required 2 guarantors (Hoshounin 保証人) to sign alongside your rent contract. Unless you have family there, this will be fairly difficult to get from a friend. Fortunately, there are 'guarantor companies' that make a living providing a service that acts as a guarantor for people in this very situation. If your real estate agent is good, they will refer you to a guarantor company to help you. Do not find one on your own, as many require you to have a guarantor before they guarantee you (WTF does that even mean?). Furthermore, expect to pay a steep fee for their services.
Key money (Reikin 礼金) – Most listings will charge reikin in the form of 1-3 months worth of rent. The amount is disclosed on the listing and should not come as a surprise. It is important to understand, however, that reikin is nothing more than extra money landlords try to shake out of new tenants, and can be negotiated. Generally, you would do this by telling your real estate agent to do something about it, and at minimum they should be able to drop the amount for you.