Typically K-Visas are handled by the US consulate or Embassy in the country of residence, so if your girl friend is in Japan on a resident visa, then the consulate in Japan will handle the visa.
Note: she will need a police report from Japan if she has lived in Japan more than 1 year, as well as one from PI.
From what I read Japan is easier than PI for visas.
Just indicate on form I-129F that the foreign consulate is in Japan.
Some info:
http://tokyo.usembassy.gov/e/visa/tvisa-niv-k.html