An attempt by the Japanese delegation to force a vote on whether to end a 15-year global ban on commercial whaling was held up amid the arguments.
And Japan, angered over what it sees as hypocrisy after its own request to hunt minke whales was rejected, threatened to block a renewal of quotas for indigenous people sought by countries including the United States.
UK Fisheries Minister Elliot Morley slammed Japan's position: "Not only is it an insult to the Russian Federation and the United States, it is also throwing the whole IWC into crisis."
'Double standards'
While opposing ending the moratorium of commercial whaling, the US is pushing for an increase in aboriginal catch quotas.
Indigenous groups - including the Makah Indians on the northwestern Pacific US coast and Alaskan Eskimos - have been allowed to hunt a limited number of whales to fulfil what are termed cultural and subsistence needs.
But conservationists, as well as Japan, criticise the hunts, which target gray and bowhead whales, because these species are believed to be endangered.
"All international law and rule and science is on our side," Japanese spokesman Joji Morishita said.
"Our stance will not change."
Japan lost a vote on Tuesday to expand its coastal catch of minke whales.
But US officials say aboriginal whaling is different from Japan's request in that it has no commercial element.
"It is for subsistence only. It [the whale meat] cannot be sold. It is only for their families," said US delegtion head Rolland Schmitten.
The annual meeting, which is due to end on Friday, is already a day behind on its agenda.
'Plentiful species'
Other contentious issues, such as the commercial whaling ban which Japans wants lifted, have not yet been discussed.
Japanese officials admit they are unlikely to muster the three-quarters majority needed to end the ban, but say they want to express their dissatisfaction with the current situation.
Japan, which argues that many whale populations are plentiful enough to allow limited kills, says the catches it seeks would be different for each whale species.
But opponents, including the US, say that abuses are likely due to the difficulty of monitoring the number and species of whales killed.
US delegation spokesman Scott Smullen said: "For the past 13 years [the Japanese] have tried similar proposals, for 13 years they've failed."