The proposal, presented to the IWC at a informal meeting in the US over the weekend, would allow Japan, Norway and Iceland to openly hunt whales despite a 1986 moratorium on commercial whaling but aim to reduce the total catch over the next 10 years.
Anti-whaling group Sea Shepherd said New Zealand had given into extreme pressure from Japan.
"This government should figure out who it represents, the people of New Zealand or the people of Japan," Sea Shepherd captain Paul Watson said.
Australia has rejected the proposal and said it will go to the International Court of Justice if negotiations fail.
Sir Geoffrey said New Zealand and Australia had the same aims, and both countries still opposed so-called scientific whaling, especially in the Southern Ocean.
"At the moment we're in negotiations and the negotiations are not finished, we don't know where it will end up," he told Radio New Zealand.
Sir Geoffrey said the proposal's main aim was to reduce the number of whales being killed by bringing scientific whaling under international control.
"We've got this great big loophole in the middle of this treaty (the moratorium) and these talks are aimed at bringing all that under international control so that no longer will nations be able to give themselves a permit to go special permit whaling," he said.
"That would be an enormous piece of progress."
Japan skirts the international whaling moratorium by using a loophole that allows "lethal research" on the ocean giants.
Japan argues that whaling is part of its culture and makes no secret that the meat winds up on dinner plates.
The compromise would bring scientific whaling under the control of the IWC, requiring Japan to submit DNA samples and other data to the 88-nation body.
Norway and Iceland defy the moratorium on commercial whaling altogether by lodging objections to the international decision, a practice that would be banned under the compromise.
Sir Geoffrey said all diplomatic processes needed to be explored before going to the International Court of Justice.
"It's a very uncertain prospect that the case has, and if it was lost I think the chances of making progress in the future would be very limited indeed. It's quite possible that the International Whaling Commission could break up altogether.
"We are particularly interested in New Zealand in saving the International Whaling Commission because we thinking that's the best way of saving whales."
