Based on the Immigration Control and Refugee Recognition Act, in principle a foreign national wishing to enter Japan is required to have a valid passport issued by the government of their own country with a visa issued by the Government of Japan.
The visa indicates that it is appropriate for the foreign national to enter and stay in Japan. Furthermore, holding a visa is only one of the requirements for entering Japan and does not guarantee that the holder of the visa will be able to enter Japan.
Visas are issued in the Japanese embassy or consulate in the foreign country. Visas cannot be obtained after arriving in Japan.
The immigration officers check whether or not the foreign national wishing to enter Japan meets all the requirements for entering Japan stipulated in the Immigration Control and Refugee Recognition Act. The requirements include having a valid passport and visa, the purpose of entering Japan, and the planned length of the stay. If the requirements are met the immigration officer grants the foreign national "landing permission" (which is then stamped in the passport of the foreign national).
The "landing permission" stamp displays the "status of residence" showing the activities, etc. the foreign national can engage in while in Japan and the "period of stay" which is the length of time that the foreign national can stay in Japan.
The visa immediately becomes invalid once "landing permission" has been granted (Note), and the "landing permission" becomes the legal basis for the stay of the foreign national in Japan.
(Note) Multiple visas remain valid until the date of their expiration.
People commonly talk about "switching the type of visa" and "extending a visa" but in law these actions equate to a "change of status of residence" and an "extension of period of stay" respectively, and applications are accepted by the Ministry of Justice (the Regional Immigration Bureau).
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