There are many websites that one can use to scout for a place in Japan depending on the type of accommodation that you are looking for.
Here are some websites that I have personally used:
They offer share house, apartment and dormitory type of accommodations. Their website is really easy to navigate and everything is easy to understand. While share houses are usually well furnished, their apartments are also furnished! This is really helpful for foreigners like me because most apartments are unfurnished and one would have to fork out extra money to buy furniture or electrical appliances.
They offer share house, apartment and social residences. As with Sakura House, their website is also easy navigate thanks to the English language option tab.
Social Residence is an interesting concept for me. In Malaysia, we're used to share houses but social residence is like a super share house!
Social Residence emphasizes on community. Some have gyms, movie room, study room or music room. So there's really a lot of space for use to cultivate your hobbies. Plus because many people will be sharing common areas such as the living room or the kitchen, it reminds me of a back packer's place where you get to mingle and make friends with many different people.
This website was introduced to me by my real estate agent. Unlike, the first two, this is a Japanese only website. At Home's, you can not only rent, but buy, sell and build!
I used Home's the most while searching for an apartment. While there are some that are furnished, many come unfurnished.
I like the map function the best because I get to zoom in into the area that I'm interested in and check if there are any accommodations nearby for rent.
There are both the Japanese and English version to the website. This website is easy to use thanks to the refine search section on the top right which is very extensive. You can use it to pin point to the exact requirements that you want.
This is a Japanese website and like Home's, you can not only rent, but buy and build too! Again, very easy to use. I usually select the nearest train station that I am interested in and start from there.
Of course there are many other English websites that one can easily google online, but I have not much experience with them so I can't comment on it.
Anyways, in my case, I got into contact with my real estate agent through a friend's friend late last year. As the date of my departure to Japan got closer, she shared with me links of some of the rooms which she felt matches my requirements, and I also showed her some of those that I was interested in. However, many of those that I was interested in do not rent to foreigners. Plus because I started scouting for apartments few weeks before, some of the apartments were already rented by the time I arrive in Japan. My agent said that during the time when I was seeking for a place was the time where many people were also moving.
So we set up a date where she brought me to view several different apartments. From there I picked one that I liked best and proceeded with it. She explained to me the fees that I would incur and submitted my documents.
Not having a phone line is really an inconvenient thing in Japan. Without it, the guarantor company couldn't contact me but we eventually sorted that out. I had to talk with both the guarantor and management company before they evaluate to rent the place to me or not. When all that got sorted out, I had to bank in the payment to them as well as my agent before getting my keys.
Other than the problem with the phone, banking in was also a problem because I didn't have a bank my address registered yet. I tried to register it in the morning but the lady said that since I have not move into the apartment yet, I couldn't register it. I was pretty flustered at that moment because banks close at 3pm and I needed to bank in the money on that day. Thank goodness, S happened to be in Tokyo when I contacted him for help. So we headed to the main branch and made the payment using his identity instead. I sent the receipt to my agent and yes, it's done!!!
The procedure was ok I guess. I went to view the apartments, decided on an apartment the next day, spoke to the companies 2 days later, submitted the payment another 2 days later and went to collect my keys 4 days later.