Do I need a transit visa for a layover of 12:45h (from morning to evening) at Haneda Airport?

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Timatic, the database used by airlines to check documentation requirements, says:

Transit Countries

Japan

Passport

Warning:

Passengers must have a negative COVID-19 test taken at most 72 hours before departure from the first embarkation point. Tests accepted are: CLEIA/ECLIA quantitative antigen test, LAMP, NEAR, Next Generation Sequence, PCR, RT-PCR, Smart Amp, TMA or TRC. The test certificate must be in English and specify that the test is based on a "nasopharyngeal swab", or "saliva", or "nasopharyngeal and oropharyngeal swab". A "nasal swab" is also accepted if the test type is LAMP, NEAR, PCR, RT-PCR, Smart Amp, TMA or TRC. Details can be found at https://www.mhlw.go.jp/stf/covid-19/border_test.html and https://www.mhlw.go.jp/content/000905811.pdf

Visa

Visa required.

TWOV (Transit Without Visa):

Passengers with a confirmed onward ticket for a flight to a third country on the same calendar day. They must stay in the international transit area of the airport and have documents required for the next destination.

Passengers transiting through Tokyo (HND) or Osaka (KIX) with a confirmed onward ticket for a flight to a third country within 72 hours. They must stay in the international transit area of the airport and have documents required for the next destination.

(... goes on about shore passes etc. ...)

So the general rule for Indian citizens is that they don't need a transit visa if they stay in the "international area of the airport" (aka airside) and have a flight to a third country on the same calendar day.

When transiting in HND or KIX, this is extended to 72 hours.

So in your case, no, you should not need a transit visa.

You may want to check on the IATA travel centre which is another interface to Timatic, entering your actual flight dates and details, as there may be rule changes in the near future which are not taken into account by the Emirates interface for instance.

Rules for Japan have changed a lot over the last few months/years due to Covid, but have been relaxed recently, this may be the reason the airline agent is asking for this. Ask them to double-check Timatic.

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