@moffintosh We don't know. They don't keep track of ethnicities.
However foreign residents make up 2,3% of the population and if I did my math correctly there's about 5500 foreign residents from Africa and about 25000 blacks from US and Brazil (assuming they reflect home population) which means black foreign residents make up about 0,025% of the population.
And since Japan has always been xenophobic and is very far any large black population the amount of black citizens is statistically insignificant.