In general, to get a visa to work in Japan, you apply at the Japanese embassy or consulate responsible for your area after receiving a Certificate of Eligibility (COE).
People already in Japan usually apply for permission to change status of residence at a Regional Immigration Services Bureau, instead of applying for a visa at a Japanese embassy overseas.
Certificate of Eligibility (COE)
This certificate is issued by a regional immigration services bureau in Japan after checking in advance whether the activity you will do in Japan matches the residence status. In many cases, the accepting company or an application agent completes the procedure in Japan.
Visa
This is something you apply for at a Japanese embassy or consulate overseas in order to enter Japan. Even with a COE, visa issuance and entry into Japan are not guaranteed.