daydreamer_now
Is it hard to find a place in japan or does it depend on what city you want to live in???? This is going to sound like a cop out to some people but the answer is "Yes and No" to both parts of your question. Seriously.
There are plenty of apartment finder services in Japan (very similar to real estate agents) and they keep huge lists of different types of apartments in different locations (and cross referenced) to try and meet your needs. Do you want a 1LDK (living dining kitchen with a bedroom) or a One Room Mansion where everything except the bathroom is in the same room? Do you want it close to a train station (more expensive) or near the grocery? These are a few of the questions you have to answer as the agent narrows your selection down. Price range?
Then there is the matter of "Key Money" which is like 3 months rent up front to the apartment owner just for the privilege of moving into his building. Often this is non refundable when you move out. Some apartments don't ask for Key Money at all.
Then there are a few apartments that don't allow foreigners. We're too noisy for their standards. There will be a few apartment buildings in the big cities set up for foreigners but they are often owned or operated by large English school chains.
All of my experience in Japan is in the Osaka, Kyoto, Kobe area (aka Kansai area) and the smaller cities in-between (Itami, Minoo and Amagasaki). One of the easier ways to get started looking for apartments there is to pick up a copy of the English language magazine
Kansai Time Out at the biggest bookstore in Osaka (Kinokuniya in the Umeda section of Osaka). Or you can check their online site
http://www.japanfile.com/modules/news/Hope this helps some. Japan is a great place to live if you can afford it but you have to put up with some major headaches getting set up while not getting ripped off at the same time.