Sea Shepherd said it had located all five Japanese vessels and was now in pursuit, forcing the harpooners to cut short their operation and retreat.
The group released footage and photographs showing three minke whales dead on the deck of the factory ship Nisshin Maru and said a fourth, also believed to be a minke, was being slaughtered when Sea Shepherd's helicopter flew overhead.
"There's three carcasses on the ship, a fourth carcass has been cut up. There's blood all over the place, meat being carted around on this factory ship deck, offal and innards being dumped in the ocean," said Sea Shepherd Australia chairman Bob Brown.
When the Nisshin Maru was first spotted from the air Brown said it was in Antarctica's Ross Dependency, within New Zealand's territorial waters and the Southern Ocean Whale Sanctuary, which he described as a "gross breach of international law".
The commercial hunting of whales is prohibited in the sanctuary, which was designated by the International Whaling Commission (IWC) in 1994, but Japan catches the animals there under a "scientific research" loophole in the moratorium on whaling.
Japan's fisheries agency said its programme was being conducted "in line with a research plan submitted to the IWC".
The Japanese foreign ministry said research whaling was "not a violation or an abuse of a loophole in the international convention".
"Quite the contrary, this is a legitimate right of the contracting party under Article VIII of the International Convention for the Regulation of Whaling", it said.
Brown described "massive violence" against the whales, using grenade-tipped harpoons to catch them, and said Sea Shepherd would do "all it peaceably can to prevent this grotesque and cruel destruction".
"There is nothing scientific about this, it is butchery," Brown said.
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