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The commission's new chairman said the IWC should now question its role as the conference on the Portuguese island of Madeira wrapped up a day early with delegates agreeing only to extend negotiations on whaling for another year.
"We have to re-establish a consensus on what the IWC is and should do, and there are at least two contradictory perceptions to answer that question," said Cristian Maquieira, who was elected chairman during the talks this week.
Joji Morishita, a senior official with the Japanese delegation, said the commission should approve limited commercial whaling by next year, adding: "Without that... the future of the IWC is seriously in doubt."
Conservation groups were also angry, with Greenpeace saying: "After 12 months of talking... all the IWC has achieved is another 12 months of talking."
The Whale and Dolphin Conservation Society (WDCS) said it "deeply laments the fact that not a single of the important whaling topics was resolved."
The IWC was set up in 1946 by 15 whale-hunting nations in order to manage a whale population that was being threatened by the fishing industry. The body now has 85 members and has taken an increasingly conservationist approach.
In 1986, it instituted a ban on commercial whaling that still stands today.
The commission has been deadlocked in recent years by divisions between countries such as Japan that say the dangers of whaling are exaggerated and other nations like Australia which want the whaling ban to be kept in place.
Maquieira said a compromise was "not impossible" but would be very tough.
In a further sign of divisions, delegates failed to agree Thursday on whether Denmark could resume limited hunting of humpback whales off the coast of Greenland as part of "aboriginal" subsistence hunting by local communities.
"As it has not been possible to reach a consensus on Denmark's request, an extraordinary meeting will be organised to discuss the matter again," Portuguese commissioner Jorge Palmeirim told AFP.
"There is no other option but to postpone the matter," he said.
Denmark had proposed to hunt 10 humpbacks a year off Greenland, a semi-autonomous Danish territory.
Environmental campaigners, who are against Denmark's proposal, were angered by the failure of the countries present to vote on the issue.
Commercial hunting of humpbacks has been banned since 1966 but Greenland continued to capture the marine mammals until 1987, when the moratorium was extended to "aboriginal" subsistence hunting.
Some European delegates at the IWC conference had deemed the proposal unacceptable, arguing that Denmark had failed to prove that Greenland's native Inuit populations had greater need of whale meat.