Scientists appointed by the commission have spent years devising a foolproof method for selecting how many whales can be harpooned while guaranteeing to keep stocks at a healthy level.
However, at last month's annual meeting of the IWC in Kyoto, Japan, the commission declined to adopt the work of its scientific committee on the Revised Management Procedure for whaling.
'The reasons were nothing to do with science, they were political,' Philip Hammond, of Britain's Marine Mammal Research Unit in Cambridge, told the Independent yesterday. He has quit as chairman while remaining on the committee.
The commission is dominated by an anti-whaling majority, led by nations such as the US, Britain and Australia - known as the 'like-minded group'. Facing pressure from environmental and animal welfare bodies such as Greenpeace and WWF, the group's aim is to stretch out the IWC's 1986 moratorium on commercial whaling indefinitely, however healthy the level of whale stocks.
Dr Hammond, an expert on whale, dolphin and seal populations, emphasised that adopting the Revised Management Procedure did not commit the IWC to ending the moratorium. Before it can be lifted the commission will have to hold difficult debates on whether whales can be killed humanely and what type of international observer scheme is needed to ensure a nation's whaling fleet does not kill more animals than its quota.
Dr Hammond said it took years of intense argument and high-powered thought within the 100-strong committee to devise a Revised Management Procedure which secured its unanimous backing. 'The future of this unique piece of work, for which the commission had been waiting for many years, was left in the air,' he wrote in his resignation letter to the IWC's secretary, Dr Ray Gambell.
'What is the point of having a scientific committee if its unanimous recommendations on a matter of primary importance are treated with contempt? The morale of the committee is lower than at any other time.'
Dr Hammond said he had spent more than a third of his working time in the past year on scientific committee tasks. 'Given the outcome, I can no longer justify that amount of time to myself or my employer,' he said.
The highly complex Revised Management Procedure would not allow any population of whales to be caught if their numbers fell to less than 54 per cent of their natural level before hunting began. It would also set quotas which would allow populations to climb to more than 70 per cent of the pre-exploitation level.
Dr Hammond's resignation will give some comfort to Japan and Norway, the pro-whaling IWC nations. The Norwegian government is defying the IWC, allowing its whalers to catch 296 minke whales in the north-east Atlantic this year - 160 for commerce, 136 for scientific research. But the country's whaling fleet has been beset by bad weather. So far, only four have been killed.