Japan's whaling fleet has clashed with anti-whaling group Sea Shepherd, which was attempting to disrupt a hunt in the Southern Ocean, say the activists.
Sea Shepherd said a Japanese ship deliberately rammed three of its boats and threw concussion grenades at them.
Japan's Fisheries Agency blamed Sea Shepherd for the incident.
Japan hunts whales each year as part of what it says is a scientific research programme - its fleet has frequently clashed with activists who follow it.
The Fisheries Agency said the activists had ignored warnings from the Japanese vessels and hit the Nisshin Maru a number of times.
It accused Sea Shepherd of carrying out a "dangerous act that threatened the safety of our research fleet and lives of its crew".
Bob Brown, director of Sea Shepherd, said Wednesday's clashes had been the worst since 2010, when the group's flagship Ady Gil trimaran was badly damaged and sank.
He said the crew of Sea Shepherd's Bob Barker had been trying to prevent the 8000-tonne Nisshin Maru from refuelling - from the South Korean-owned Sun Laurel tanker - when it was "repeatedly rammed" by the Japanese ship.
He said the Nisshin Maru had fired water cannon at the Sea Shepherd vessels and that its armed escort had "lobbed concussion grenades onto the decks" of the Australian-flagged ships.
A statement on Sea Shepherd's Facebook page said its Steve Irwin and Sam Simon vessels were also rammed, but that it was the Bob Barker which had suffered the most damage, at one point being sandwiched between the whaling ship and the Sun Laurel.
The Bob Barker issued a distress call after it lost power and began taking on water, but the crew were able to regain control. No injuries were reported.
Sea Shepherd said it was now escorting the Sun Laurel, as its lifeboats were damaged in the incident.
The director of Sea Shepherd Australia, Jeff Hansen, said the Nisshin Maru had "committed the maritime equivalent of a hit and run accident. They have rammed the Sun Laurel, putting them in perilous danger, and simply abandoned them".
Sea Shepherd says the incident happened inside Australian waters and inside the international Antarctic Whaling Sanctuary.
"This is grand piracy, a complete breaching on a number of fronts of international and Australian domestic law," said Mr Brown, who is also a former Australian Greens senator.
He called on Australia to despatch naval vessels "not just to film the slaughter of the whales by the Antarctic fleet but to restore international law".
Australia's Environment Minister Tony Burke said he was aware of the reports and was seeking more information.
"The government condemns so-called scientific whaling in all waters and we urge everyone in the ocean to observe safety at sea,'' he said in a statement.
Australia is taking legal action against Japan over whaling.
There has been an international ban on commercial whaling for 25 years, but Japan continues to catch hundreds of whales each year.
Tokyo says the whales are part of a scientific research programme, but critics say it is commercial whaling in another guise.