Determine a reason for immigrating to Japan. Steps will be different from a person immigrating for education and work than for simply visiting in the short-term.
Get a passport. Upon arriving in Japan your passport will be stamped with status of residency such as worker, student or tourist. This will indicate what you are allowed to do while in Japan.
Get a visa. For a work visa you will need to apply at the Japanese embassy upon arriving in the country or go to a Japanese consulate before traveling. The work visa is good for three years. In order to study in Japan, you will need to get a letter of acceptance from a university first. You must show proof to the university that you have enough in your bank account or parents account in order to support you for one year in case of an emergency and for school costs. The university will then request a certificate of eligibility from the Ministry of Justice. Upon acceptance, the Ministry of Justice will send the university the certificate and the university will send you the certificate. Upon arrival you will need to show the Japanese consulate the certificate and acceptance letter in order to receive a student visa which is good for one year.
Renew your visa. In order to stay longer you must apply at the Japanese consulate for an extension. For a work visa, an extension can be renewed every three years for as long as you live in Japan. For students, the renewal would have to be done every year up to four years.
Get fingerprinted and photographed. Upon entering Japan you will need to meet to these requirements in order to be allowed into the country. Those excluded are residents/citizens, children under 16-years-old, diplomats, and those individuals that lost their citizenship through war.