You're misunderstanding slightly. The toothed whale species that eat other fish are the ones that have the problems with high mercury & PCB content.Also, from what I've read whale meat can be highly toxic (pollutants such as mercury, PCBs).
Krill-eating whales don't have the same problems, and from what I understand taste a bit different too.
Every nation I know fishes miles away from their own territorial waters - high seas fishing. Why shouldn't Japan as well?