If you’re in Tokyo, you will be dealing with the Tokyo Regional Immigration Bureau office. This is place you go to pick up and deliver forms and get those all-important stamps in your passport. Unfortunately it’s in Shinagawa, not near the station, which is very inconvenient unless you actually live nearby. The Immigration Information Center inside the Bureau has a useful telephone help line though.
They have staff speaking a variety of languages. Every time I phoned, I got an English speaker, and of course they also have Korean, Chinese and several others. However, while the information staff tend to be multilingual, many of the people who actually process your forms speak Japanese only. If possible, take a Japanese speaker to help. It’s not essential though — I managed all right by myself, so it can’t be too hard.
If you’re not near Tokyo,you’ll have to find your own local Regional Immigration Bureau. The Ministry of Justice has a list of immigration offices throughout Japan.