The organisation in charge of Japan's scientific whaling programme has accused the Sea Shepherd Conservation Society of endangering its crews in the Southern Ocean.
The two sides have clashed for the first time during this season's Antarctic hunt.
Sea Shepherd says it is determined to pursue the Japanese whaling fleet through the icy waters of the Antarctic.
It says the whaling ships used water cannons on their inflatable boats during high-speed chases.
But the Institute of Cetacean Research has accused the Sea Shepherd activists of throwing glass bottle projectiles and deploying ropes to try and foul the propeller and rudder of one of its ships.
It has accused the group of dangerous and violent tactics, and is calling on Australia to take criminal action against the activists reports the ABC.
Two groups clash in Southern Ocean
Sea Shepherd's founder Paul Watson says his three-strong fleet located the whalers in the Southern Ocean on Friday before they could start hunting.
On Saturday, inflatables launched by the protest fleet got between three Japanese harpoon vessels and the factory ship Nisshin Maru amid ice floes 3000km south-east of New Zealand.
Mr Watson says the Japanese fired a water cannon and stink bombs were thrown onto the decks of the whaling ships.
The protest fleet resumed its pursuit of the Nisshin Maru, with the Japanese harpooners pursuing the protesters in turn, he says.
"Once we are on the Nisshin Maru we're just going to block it to prevent their whaling operations. We do know they are not whaling because all three harpoon vessels are chasing after us instead of chasing whales.
"We're trying to get a zero quota here and make sure they don't kill any whales."
The Japanese fleet left for the Southern Ocean at the start of December.
The governments of New Zealand, Australia, the Netherlands and the United States in December jointly condemned in advance any confrontations that could threaten human life, and called on both sides to act responsibly.
The governments say they are disappointed that the Japanese fleet intends to hunt whales again.
Commercial whaling has been banned worldwide since 1986 but Japan justifies its annual hunts in the Southern Ocean as lethal scientific research.