Prime Minister John Key said New Zealand's ambassador to Tokyo delivered a "strong" formal message from 33 countries, including the United States and Australia, to Japan.
"We consider that there is no scientific basis for the slaughter of whales and strongly urge the government of Japan not to allow it to go ahead," Key said in a statement.
A Japanese whaling fleet set sail for the Antarctic last week, despite environmentalists slamming the move as a "crime against nature".
The fleet's departure marked the end of a year-long suspension prompted by a United Nations' International Court of Justice (ICJ) ruling in 2014 that the annual hunt was a commercial venture masquerading as research.
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Australia, which hauled Japan before the ICJ in 2010 in a bid to end the annual hunt, would continue to raise concerns, Foreign Minister Julie Bishop said.
"We are working with other like-minded nations to build international consensus against Japanese whaling," Bishop said in a statement.
Tokyo claims it is trying to prove the whale population is large enough to sustain a return to commercial hunting, and says it has to kill the mammals to carry out its research properly.
However, it makes no secret of the fact that the animals' meat ends up on the dinner table or served up in school lunches. New Zealand, which said Mexico, South Africa and EU member countries also joined the formal protest, said it would press for an end to "this outdated practice".
Australia made clear lethal research was unnecessary.
Environmentalists from Sea Shepherd Australia have vowed to pursue the Japanese fleet and aim to intervene in any slaughter of the animals, as it has done for the past decade.
Their vessel the Steve Irwin was due to leave Melbourne on today evening for Western Australia, before it leaves for the Southern Ocean on a mission to halt illegal fishing.