There are around 500,000 minke whales (the type they hunt) in the Antarctic, Japanese whaling kills approximately 300 whales per year.
Please explain to me why you think this is such an issue?
The problem isn't primarily about the numbers of minke whales. It's that they are hunting what many people consider a sentient species, in an inhuman way. In most parts of the world, you aren't allowed to slaughter an animal (at least in theory) in a way that causes pain or distress. With whales there is no reasonable way of doing this due to their size.