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First time for me to fly international.
I have Philippine passport booking separate roundtrip tickets from Manila to Narita (with Philippine Airlines) and Narita to San Lucas (Cabo), Mexico (with Aeromexico Airways).
PAL flight from Manila will arrive at Terminal 2 and Aeromexico flight will depart from Terminal 1.

I just wanted to make sure I won't be held up by the Immigration, should I get a TRANSIT VISA for a 3 to 4 hours layover in Narita Airport, transferring from Terminal 2 to Terminal 1?

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You will need a transit visa, not because you're changing terminals (you don't need it for that) but because 1. you need to collect your luggage and 2. At the departure airport the staff will consider Tokyo your destination because your other ticket is separate.

If you were transiting overnight, you could enter for up to 72 hours without a visa:

Visa required, except for Holders of onward tickets transiting to a third country can obtain a Shore Pass on arrival for a max. stay of 72 hours only if there are no connecting flights on the same calendar day

However, seeing as it's a same-day connection, you do need a transit visa.

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