Japanese whalers are accusing activists from the Sea Shepherd Conservation Society of throwing illegal stun grenades at their fleet in the Southern Ocean.
Sea Shepherd says its pursuit of the fleet has so far disrupted this season's whale hunt, the ABC reports.
Japan's Institute of Cetacean Research, which organises the annual hunt, has released footage taken on Sunday which it says shows Sea Shepherd activists throw two stun grenades, also known as flash bangs, and a smoke bomb onto harpoon ship Yushin Maru No 2.
The institute says at least one of the grenades landed on protective nets on the harpoon ship.
But Sea Shepherd founder Paul Watson says the group only uses harmless smoke and stink bombs in their mission to prevent the killing of whales.
"We couldn't have thrown flash bangs on the ship - we don't have them, it's prohibited. We couldn't even bring them into Australia if we wanted to. So they certainly don't have any evidence of us doing that, because we simply didn't do it."
Mr Watson says his group's pursuit of the Japanese fleet has resulted in few, if any, whales being killed so far this season.
Commercial whaling has been banned worldwide since 1986 but Japan justifies its annual hunts in the Southern Ocean as lethal scientific research.