Footage of the ships colliding
The Sea Shepherd activists' anti-whaling ship, the Steve Irwin, has collided with Japan's Yushin Maru 2 harpoon vessel in Antarctic waters.
Japan condemned the collision as an "unforgiveable act of violence". The activists said it had been unavoidable.
Damage occurred to the ship's railing but no injuries have been reported.
The radical anti-whaling group has been pursuing the Japanese whalers since December and confrontations have increased in recent days.
Japan is allowed by the International Whaling Commission to harvest 935 minke whales and 50 fin whales this season for research purposes.
Activists say Japan kills the whales for commerce, not science.
Paul Watson, captain of the Steve Irwin, said his crew was trying to block the transfer of a dead whale from the harpoon vessel to the whalers' factory ship, the Nisshin Maru.
"We were in the process of blocking the transfer from the Yushin Maru 2 when the Yushin Maru 1 moved directly in front of the bow to block us," Mr Watson said in a statement.
It is an act of violence and it is unforgiveable
Japanese fisheries ministry
"I could not turn to starboard without hitting the Yushin Maru 1. I tried to back down but the movement of the Yushin Maru 2 made the collision unavoidable," he said.
"It is an act of violence and it is unforgiveable," said Shigeki Takaya, an assistant director of the Far Seas Fisheries Division at Japan's fisheries ministry.
"We will ask concerning countries, including Australia, to immediately stop them from carrying out such horrendous acts," he said.
Chiharu Tsuruoka, a Japanese foreign ministry official, noted that the Steve Irwin is a Dutch-registered ship.
"We have repeatedly asked the Dutch government to stop them from harassing us, but so far it's been so unsuccessful," Mr Tsuruoka said.
Chaos and friction
The incident caps several days of increasing friction between the activists and the whalers.
On 6 February, two protesters said they had been injured in the Antarctic after they clashed with Japanese whalers, but a whaling official said the ship's crew only used water cannon in self-defence.
Japanese whalers fire water cannon at conservationists
Japanese officials said the Sea Shepherd group had been throwing bottles of butyric acid, a product of rancid butter, at the Japanese ships.
Mr Watson said the Japanese had responded by blasting his crew with a water cannon, hunks of metal and a "military grade" noise weapon that can cause deafness and vomiting.
He said several of his crew have experienced headaches from the noise device.
"The situation down here is getting very, very chaotic and very aggressive," Mr Watson told the Associated Press news agency, speaking by satellite phone from the boat.
The Sea Shepherd Conservation Society has been blamed for collisions with the Japanese Antarctic whaling fleet in recent years, as well as high-seas boardings and stink bomb attacks.
Japan says it kills whales for research, but critics say the goal is consumption
Both the Australian and New Zealand governments oppose the Japanese whale hunt, but have called on whalers and anti-whalers to remain peaceful in the dangerous Southern Ocean.
Although Japan officially stopped whaling under a 1986 global moratorium, it continues to take hundreds of whales under a loophole allowing whaling for research purposes.
Much of the meat ends up on supermarket shelves and dinner tables.
Protesters set off from Australia in early December, chasing the whaling fleet for about 3,200 km (2,000 miles) before stopping two weeks ago in Tasmania to refuel.
The group found the whalers again on Sunday and resumed their pursuit.