My sister is planning to return to Japan this January 2022, and she is a Japanese citizen. She has no choice but to land in Tokyo (Haneda or Narita) and she lives in Kyoto. Under quarantine measures, how is she able to make it home to Kyoto and avoid quarantining in Tokyo? She does not have a drivers license, so she cannot rent a car. Are there affordable shuttle services from either airport to Kyoto?
If she is planning to quarantine with friends or family in Kyoto, then they are allowed to pick her up and drive her back. Otherwise, to the best of my knowledge, the only options are a very expensive private driver all the way to Kyoto or quarantining closer to Haneda.
Kansai International airport seems to have the same covid transport services as Haneda, so she could possibly take a domestic flight from Haneda to Kansai International, and then get a special taxi (booked well in advance) to Kyoto from there. Her local Japanese consulate could probably provide confirmation as to whether that will be possible.
Quarantine restrictions don’t allow international arrivals to take domestic flights. You have to leave from your port of arrival. Of course Elisa’s sister could fly directly into KIX, which would probably be easier even if it’s a bit more expensive.