People have been asking that question for 20 years, but mostly for reasons that have nothing to do with whaling or conservation.
The most likely reasons - as clearly explained in the paper linked by Eric - are a mix of different value systems and national pride. Japan's approach to whale conservation is purely scientific - they have little time for the touchy-feely 'whales are special' approach. So if the stock assessment says whales can be exploited then, as far as they are concerned, that's the end of story. I have to say - whatever your views on whether some whales stocks are suficiently robust or not at the moment (and some of the findings appear to be far from cut and dried) - many of the NGOs lobbying on the IOC do rather shoot theirselves in the foot when they say fairly explicity ' Yes the scientific finding are important - but only if they support our case.. If they don't then scientific stock assessment doesn't matter 'cos whales are special.' You can't really cherry-pick the data you like and expect your interpretation of the data to be views as a fair and accurate representation.
The second point seems to be national pride - no country likes to be told to mend their ways by other countries purporting to hold the moral high ground. If it appears they are being bullied into it, they are likely to dig their heels in. So to respond to Dean's point - Sea Shepherd's campaign doesn't stop whales being killed, all the evidence indicates it has exactly the opposite effect. Whatever Mr Watson's motives, the end result of his campaign is to deepen Japanese resistance to allowing whaling to end for purely economic reasons and to prolong the campaign and fill the coffers of Sea Shepherd So if you are pro-whaling, best option is to donate to Sea Shepherd.