Actually, this is incorrect if I recall correctly. I seem to remember seeing some data about "incidental" kills of whales that were not accounted for in allotments. Fishing net drownings, collisions with boats and, I think, one other weird one that left perfectly usable dead whales who had died is ways that were difficult to prove or disprove and were not accounted for at all.
It was a lot of whales and not just Japan doing it.