The Japanese Ministry of Justice’s Immigration Information Center is the best place to call for all immigration related issues. It’s located in Tokyo inside the Tokyo Regional Immigration Bureau, but you can call them from anywhere in Japan (or, presumably, from outside Japan). The staff there speak a variety of foreign languages.
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.
Your first point of contact regarding Japanese visa eligibility is your local Japanese embassy. If you are already in Japan, you may want to contact your home country’s embassy. There are official lists for both of these. These are the places you need to contact for official information about your Japanese work visa and other Japanese immigration issues.
The Visa section on the Japanese Ministry of Foreign Affairs website has all the official information about Japanese immigration, visa requirements and so on. This includes entering Japan, applying for visas and other important topics for foreigners interesting in working in Japan.