The Sea Shepherd Conservation Society said that its futuristic powerboat, named the Ady Gil, was cut in half by the Shonan Maru No 2, a Japanese security ship, as it neared the whaling fleet.
The whaling crew said the boat was launching projectiles.
"All six crew were rescued, but the $1.37 million carbon-fibre trimaran is taking on water," Jeff Hansen, the Australian director of Sea Shepherd, told Al Jazeera.
"We believe it was deliberate. Our ship had come to a complete stop and they basically came straight down on top of them. They cleaned them up."
Hansen said the incident occurred after two activist vessels intercepted the Japanese fleet near Antarctica's Commonwealth Bay.
Japan's Institute of Cetacean Research, which supports the whaling programme, blamed the protesters for the collision.
"The Ady Gil came to collision-distance directly in front of the [ship's] bow," the institute said in a statement.
"The [ship] started its water cannons and proceeded to prevent the Ady Gil coming closer."
The Ady Gil, capable of a speed of 50 knots, circled the globe in a record 60 days when it was still known as Earthrace.
The vessel was renamed Ady Gil after the US multimillionaire who helped buy it for Sea Shepherd.
Japan's government-backed whaling fleet aims to harpoon up to 935 minke whales and 50 fin whales, classified as endangered, in the Southern Ocean during the current Southern Hemisphere summer.
Commercial whaling was banned under a 1986 treaty.
But the Japanese continue to cull whales on grounds that it is for research purposes and to monitor their impact on fish stocks.