Japan doesn't have much of a refugee problem at all. They pretty much learned their lesson with Korea decades ago. They have a Korean population now, which while mostly are fine residents, some have a distinct leaning towards North Korea - hard to believe but true. They're monitored of course, but that is what the Japanese get for being gracious. They haven't been keen on refugees since and are definitely not interested at all. Japan is fine as it is....doesn't need violent, demanding, unwanted blow-ins.
There are Muslims in Japan, around a 100,000 - maybe a bit more. Most from south-asia, Pakistan, India, etc....something around ten percent are Japanese converts - mainly Japanese wives of this migrant group. Being Japan, and their agencies always on the ball....they do keep an eye on this minority. As a precaution. There have been no problems of note....probably as much to do with the heritage of the migrants (not Middle-east for the most part)....and the fact that these migrants know they are definitely up against it - if they do the country wrong.
