Under Japan's Immigration Control and Refugee Recognition Act (hereafter referred to as the Immigration Control Act), it is stipulated that any foreigner wishing to enter or land in Japan must possess a valid passport and a visa obtained from an embassy or consulate. In other words, when foreigners apply to an Immigration Inspector (immigration officer) at a port of entry or departure (hereafter referred to as a port of entry) of an airport or seaport for an examination for landing, one of the conditions that they must meet is possession of a valid visa.
In principle, foreigners wishing to enter Japan are required to apply at an overseas Japanese diplomatic establishment (embassy or consulate) for a visa to be stamped in or attached to their passport valid for travel to Japan. Unless you are from a country such as the United States or Canada, which has a tourist visa agreement with Japan, you must obtain a visa before entering Japan.
Register at the nearest Japanese embassy or consulate in your country and receive a certificate of eligibility (actually a stamp in your passport indicating the proposed status). You must arrive in Japan within three months of the date of issuance. It is extremely important that you have this stamp when entering Japan; otherwise you will probably be asked many questions upon arrival and sent back home on the next flight. There are different requirements for different nationalities, so make sure you find out all the relevant information for your own case (for example, U.S. citizens do not have to apply for a tourist visa at a Japanese embassy in the U.S. since they are automatically granted a ninety-day visa upon entering Japan; but make sure this rule is still in effect before you leave).
If you are already in Japan under a tourist visa you must leave the country in order to change the status of your visa. Foreign nationals used to go to the Japanese embassy in Seoul, Korea, since that is the embassy closest to Japan. Lately, Japanese immigration has been enforcing the rule that one must obtain the visa from an embassy or consulate general in one’s own country. Therefore, unless you are Korean, going to Seoul may not be a good idea. It all depends on how busy the immigration officials are and what mood they are in. American citizens should keep in mind that there is a Japanese consulate in Guam.
Here we list some general information on Japan Visas; if you have any other questions please contact your local embassy or consulate for the most up-to-date information.

Criteria of Visa Issuance
Kinds of Japan Visas

1. General Visa
2. Specified Visa
3. Transit Visa
4. Student's Visa
5. Working-Holiday visa
6. Temporary Visitor's Visa
7. Employment or Working Visa

Frequently Visa Questions
Nationals of Countries and Areas with Visa Exemption Arrangements
Alien Registration
Re-entry Permission
Special Residency Requests
Immigration