I wouldn't get on the plane without a permit from USDA and a health certificate (properly worded) from the Japanese breeder or dealer. You also need to clear customs at one of the designated ports-of entry. Otherwise, the koi will have to be sent back to Japan or destroyed. Start by reading the information here....
Possible ban on koi and goldfish? URGENT!!!!!!! New Information from the USDA!
That said, if the fish are coming in as checked baggage it is very possible your customs agent will not know about the regulation. You would be breaking the law, but might get away with it. However, if the customs agent calls the US Fish and Wildlife agent over (as they often do when plants or animals are involved), then you're sunk because the USFWS guy will probably be aware of the new USDA/APHIS regulation. Don't let your palms sweat and tell us how it turns out.
-stev ehopk