"There are lots of methods that can be used, like acoustic tracking and satellite tagging and underwater listening stations, where you can conduct effective research without killing whales," Australia's environment minister Josh Frydenberg told AFP.
"Global stocks have nowhere near recovered to where they were before the whaling period."
Several other countries, including the European Union bloc, urged Japan to stop its hunts, some accusing it of using the scientific exemption as "a licence to kill".
Japan, in turn, opposes the creation of a South Atlantic whale sanctuary.
This proposal by Argentina, Brazil, Gabon, South Africa and Uruguay has the backing of the European Union and others.
"Today... there is a whale killing and catching in the (Southern Ocean), who may tell us that if a particular species begins to be depleted the whale catchers for science will not come to the South Atlantic?" Brazil's IWC commissioner Hermano Ribeiro told AFP.
"We want to avoid that. It's protection for today, protection for the future."
Countries are to vote on the sanctuary, which has been on the IWC's agenda for 15 years but voted down every time, on Tuesday morning.
It requires 75 percent of the vote to pass.
Morishita highlighted the intractability of the divide.
"One side... is supporting the total protection of whales under any circumstances, no kill, no one whale should be killed," he said.
The other, "like Japan, is supporting sustainable utilization of marine living resources including whales.
"These positions are so... fundamentally different and that is causing the difficulties or stalemate or deadlock of this organisation. Unless we address this issue in some manner we will just be repeating the same thing, meeting after meeting."
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Besides Japan and communities which received aboriginal whaling licences from the IWC, Norway and Iceland conduct commercial hunts, having submitted objections to the moratorium.
This year's meeting marks the 70th anniversary of the commission's founding, and the 30th birthday of the moratorium estimated to have prevented the killing of tens - even hundreds - of thousands of whales.
Conservationists say the creatures still face a multitude of perils, from hunters and ship strikes to getting snared in fishing gear and pollution.
"(...) It is in the interests of all of us to give back to the cetaceans their living environment," Slovene Environment Minister Irena Majcen urged delegates on Monday.
"This is something that should unite us."
Photo: The Japanese whaling vessel Shonan Maru 2 sits in Tokyo Bay. Credit: Getty Images/ Koichi Kamoshida