I am an Indian national residing in the United States of America under a non-immigrant visa. I am travelling to India via Tokyo and Singapore and returning on the same path. For Japan visas, there is a twenty-four-hour hotline for the U.S.A. that you can call +1-888-671-4583 for all visa enquiries. I got this information from the Japan Consulate General at Los Angeles’ website. The hotline is very helpful, and when I told them my itinerary, they deemed that I would be needing a transit visa for my India-going flight, but I won’t be needing any transit visa for the return flight. The general rule of thumb for Japan is that if you stay in the same airport with valid proof of connecting flight and all documents (like passport, visa etc.) then for short delays, you do not need any transit visas. This is my case while returning to the states. While going to India however, I am landing in Narita Terminal 1, and my connecting flight going to Singapore is from Haneda Intl’ Terminal and hence I need to get a transit visa. Although the rules are pretty straight-forward, I would rather just call the number if I were you. The staff is very helpful and resolved everything in 5 mins.
On a side note, the fees for getting a transit visa for Indian nationals is $1 (cash) in 2019 as given here. If you are applying from Japan’s Indian consulates for a transit visa instead, it should cost you INR 50 in 2019 (also given here).
You can transit through Japan airport, if you hold a same airline onward ticket or her code sharing sister airlines. An of course you have no intention to pass the immigration control. Otherwise you need a visa , it means that both parties stood on right.
Technically as @Crazydre mentioned, you do not need the transit visa for Japan. However since you have separate tickets, at least from my experience, you would have to do some serious convincing for the airline to check you in without the visa.
The reason for this is that the airline bringing you to Japan has no control or responsibilities over your second flight. It may be possible, for example, that the second airline cancels your second flight after you checked into the first one (due to weather, for example). In Narita – unlike AMS and many other airports – to get to the airport transit area you need to have the boarding pass, which is scanned before they let you through. They won’t let you in if your flight has been canceled, and in this case you’d be stuck in the arrival gates area.
You do not need a visa if not clearing immigration, as stated in Timatic, the database used by Airlines
TWOV (Transit Without Visa):
Holders of onward tickets transiting on the same calendar day.
Check in online and print out both boarding passes, so you won’t have to deal with any desk staff, or, if you do, they will have proof of your onward travel
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