Environmental activists and Japanese whalers both released videos on Saturday, showing a confrontation in waters 3 000 kiliometres south of New Zealand.
The Japanese Institute of Cetacean Research (ICR), authorised to catch whales by the country's Ministry of Fisheries, clashed with the Sea Shepherd Conservation Society.
Sea Shepherd alleged that the whalers turned water cannon and hoses on their crew, while whalers accuse the group of pelting their hunting fleet with "some rather unpleasant foul-smelling substances," they said in a statement.
A Sea Shepherd spokesman was unable to confirm what was thrown, but in previous years the activists have tossed rancid butter, or butyric acid, stink bombs at the whalers to make their decks unusable for slaughtering whales.
The conservationist group has been chasing the fleet in the hope of interrupting Japan's annual whale hunt, which kills up to 1 000 whales a year. Whalers accuse the activists of using dangerous tactics.
Every year, Japan and Sea Shepherd make claims of aggression against each other, but the accounts are generally impossible to verify. Their skirmishes take place in an extremely remote part of the ocean off Antarctica.
The Japanese are allowed to harvest a quota of whales under a ruling by the International Whaling Commission, as long as the mammals are caught for research and not commercial purposes.
Whale meat not used for study is sold for consumption in Japan, which critics say is the real reason for the hunts. Each hunting season runs from about December through February.
Locky MacLean, the captain of the Sea Shepherd's 'Gojira' vessel, said the society's three boats had been "dancing dangerously through the ice packs locked in confrontation with the three harpoon ships".
"It was both deadly and beautiful," he said in a statement on the society's website. "Deadly because of the ice and the hostility of the whalers and beautiful because of the ice, and the fact that these three killer ships are not killing whales while clashing with us."
"Our objective is to save the maximum number of whales and to maximise the financial losses of the whalers at the same time," Paul Watson, Sea Shepherd president, said in a statement.
However the Japan fisheries agency was quoted as saying: "The repeated obstructive behaviour against legitimate research activities is extremely dangerous action that threatens the vessels and the lives and property of their crew members."
Previously, the two sides have clashed violently; last year, a Sea Shepherd boat was sunk after its bow was sheared off in a collision with a whaling ship.
Australia has taken legal action against Japan to prevent it from hunting whales by exploiting a loophole in a 1986 global moratorium which allows whaling for research purposes.