Obtain a Certificate of Eligibility and/or a Certificate of Authorized Employment from the Japanese government. Talk to your employer for details about which documents you need. Typically, the employer files this round of paperwork for you. You will need one or both certificates before you can apply for your work visa.
Download and print the "Application for Change of Status of Residence" from the Immigration Bureau of Japan's website. Fill it out accurately and neatly. You will need to affix the appropriately sized passport photo to it.
Go to your local immigration office and take a number. When you are called to the window, submit the application with photo, passport with current tourist visa in it and the certificates you obtained in Step 1 to the immigration inspector. Your passport will be kept until the status change decision is made.
The agent will ask you to fill out a postcard with your current address in Japan. This postcard will be mailed to you when your status change has been approved or denied. It usually takes about a week to make a judgement.
When you receive the notification card in the mail, take it to the immigration office. You will be asked to pay the fee — at time of publication, 4,000 Yen (about $40) — and you can only do this by buying a "revenue stamp." Usually you can find these at post offices, book stores or at select convenience stores. The stamp will be affixed to a form and you will receive your passport with a sticker reflecting your new status in Japan.
