Both koi and goldfish come from China and asia in general, not Japan (they were just the ones to breed out the colors/types we know today). Also, just to be clear, Japan will have about as much fish variety as any lake in the midwest or northeast US. Its climate is subtropical at best at its southern tips and temperate everywhere else, so they don't have any tropicals. Most Rhinogoby and stiphodon, while available, do not tolerate tropical temperatures very well. Stiphodon, which are very common in the trade, generally prefer cooler water although southern species from places like Taiwan will fair better in tropical tanks.
Pretty sure there are some loaches from there - and I know that weather (=dojo) loaches are raised for food in Japan. The list linked by ThatGuyWithTheFish also says paradise fish are native to the archipelago.
During a visit to Kyoto a couple of years ago, we saw koi in every body of water, but no other fish. We also saw _lots_ of American red-eared slider turtles in the pond at Takaragaike park.