Of course, there are things that are cheaper. If you live as Japanese as you can, you can save some money. But rent prices are very high for a normal Japanese worker. As some people here already said salaries are very low.
Average income per age range[1]: 20s:348万円 (~34k) 30s:458万円 (~45k) 40s:586万円 (~58k) 50s:721万円 (~71k)
My ~55m2 room costs about ~1800$ without electricity etc. Since the owner recently changed for new people the price went up to ~2000$ Given it's a modern 'mansion' (apartment) with nice extras, in a very good location it's still cheap (wondering why every day.) I heard SF is crazy expensive, but that's a different problem. Most people here, even in IT jobs get about 2000 dollar per month. So where can they live? They can live in some 30 years old very tiny apartment or live outside of Tokyo and drive in 1 hour or more every day. Even if you live 30 minutes away by train, most trains coming from affordable areas are packed and you have to queue up to get into one, which can extend the commute time to an hour or more[2]. If you want to go to work by car be ready to pay around 300$ per month for a parking space.
Then, say you start a family. 55m2 won't cut it anymore. 80-100m2? Very few places. Very expensive. Most rooms here are between 20-35m2 made for singles.
Anyway, this maybe sounded negative but I love this city. All things considered, it's awesome and comfortable to live here.
[1] https://doda.jp/guide/heikin/2014/syokusyu/it/ [2] Source: co-worker