"Because conservationists could bid for quotas, whalers could profit from whales even without harvesting the animals.
"A market would therefore open the door to reducing mortality without needing to battle over whether whaling is honourable or shameful."
The number of whales hunted would depend on who bought the quota shares.
If conservationists bought all the shares, all whales could be protected. If whalers bought all the shares, whales could be hunted to an agreed, sustainable level.
The scientists estimated that the market price of a minke whale would be around US$13,000 ($16,400) and a larger, endangered cetacean such as a fin whale would cost around US$85,000 (NZ$108,000).
The researchers said that the US$25 million ($31.5 million) that environmental groups Greenpeace, Sea Shepherd Conservation Society and World Wide Fund for Nature (WWF) spent a year on anti-whaling projects could achieve the same results, or better, if it were used tobuy the whales - a move which would also reduce the organisations' carbon footprints.
"By placing an appropriate price tag on the life of a whale, a whale conservation market provides an immediate and tangible way to save them," the scientists said.
Quotas for sanctioned whaling were proposed by some anti-whaling countries in 2010 in an attempt to reduce the overall catch. But the compromise collapsed because some countries - such as Australia - and conservationists felt it legitimised commercial whaling.
Sea Shepherd captain Paul Watson echoed this sentiment yesterday, saying a quota system for whales equated to "Let's allow so many people to be enslaved so that others won't be".
"This is the 21st century. Nobody should be killing whales for any reason, anywhere."
Sea Shepherd estimated that its multimillion dollar anti-whaling campaign in 2008 saved 350 minke whales in the Southern Ocean. By the scientists' calculation, these whales could have been bought for around $4 million under a whale trading system.
The authors of the Nature article said there would be huge challenges in setting up the scheme, such as setting quotas and allocating shares, but it believed the International Whaling Commission was up to the task.