When will be the starting point of counting “72 hours before departure to Japan”?

Case A transiting through a country without immigration procedures.

Case B transiting through a country where immigration procedures are required by the domestic law.

For the case A, the starting point to count “72 hours before departure” will be the time you leave
a country from which the passenger originally departed.
For the case B, if you go out of the airport, or stay at the hotel located outside of the airport
upon transition, the starting point to count “72 hours before departure” will be the time you
leave a transit country you originally departed. Therefore, if 72 hours have passed since you
obtained a certificate at a departure country before you leave the transit country, you need to be
tested again to obtain a certificate in the transit country.
However, if you stay in the airport upon transition, the starting point to count “72 hours before
departure” will be the time you leave a departure country, which means you are not required to
obtain a certificate again at a transition country.
For example, if you travel from Sweden to Japan, transiting through Germany, the starting point
to count “72 hours before departure” will be the departure time from the airport of Sweden. If
you travel from Brazil to Japan, transiting through Mexico and the U.S.(which requires
immigration procedures), the starting point to count “72 hours before departure” will be the
departure time from the airport of Brazil, only if you don’t go out of the airport upon transition
through the U.S.

Information obtained from:  Ministry of Foreign Affairs of Japan Website