According to Article 7 of the Aircraft Fuel Tax Law, it seems that in the case of a foreign-borne aircraft, it is based on the flying ground rather than the refueled point.
In other words, even if fuel is refueled in the United States, if you return to Japan and use it only in Japan, “At the airport when you return to Japan,” the fuel whose remaining aircraft fuel tax is not taxed ” It is subject to taxation (deemed loading).
Since it seems that there are various flight methods, it seems to become clearer if you consult with the National Tax Agency on a more specific story.
For example, although the nationality of the aircraft is Japan, this time we will soon return to the United States and move to another Japanese airport due to the spot’s relationship and depart the next day, etc.