Well its also a case of foreign populations in Japan. If you are going to immigrate to somewhere, typically you want to do so where there is a large population of your own people. People try canada because there already are large ethnic groupings present which makes assimilating far easier. Since there is nobody in Japan except Japanese, speaking a language unique in the world, I think a lot of people dismiss Japan as a place to flee. Im not sure about this, but I also think that the Japanese operate fewer foreign offices around the world, and that they are usually missions, which are very small and concealed in large office buildings with small staffs. Refugees probably try to go to larger ones like the American Embassy first, rather than attempting to go to the Japanese one.

Im also not discounting the fact that Japan can be very strict with its Immigration policy. But I am not up to speed with Japanese asylum laws and practices to conclusivly say.