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This question already has an answer here:

I and my wife are visiting Sfo, USA on Indian passport and will be going back to Delhi via Tokyo, Japan by Ana airline in October. I want to see Tokyo, how to get the required transit visa on arrival?

marked as duplicate by Aditya Somani, VMAtm, Karlson, Gagravarr, choster Aug 16 '14 at 18:37

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Japan never grants visas on arrival, only landing permissions, which are not visas. You may be referring to the landing permission provided by Article 15 of the ICRRA, especially clause (2), which states

(2) An immigration inspector may, upon application by the captain of the vessel or aircraft or the carrier who operates the vessel or aircraft, grant a foreign national (except for crew members) aboard the vessel or aircraft permission for landing in transit when such foreign national wishes to proceed via Japan to an area outside Japan and to depart from Japan within 3 days of his/her entry into Japan from another port of entry or departure in the vicinity of the port at which the said foreign national entered Japan on board a vessel or aircraft other than the one on which the foreign national arrived in Japan.

So it seems the airline must make an application on your behalf, and you should probably contact them.

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