Anti-whaling group Sea Shepherd has accused the crew on board a Japanese whaling vessel of lying about the circumstances of a confrontation in the Antarctic.

Sea Shepherd has called for an apology from the Japanese Government, which claimed the activists attacked crew members aboard a Japanese whaling vessel by throwing rancid butter bombs at them.

But the captain aboard the Sea Shepherd vessel in the Antarctic, Paul Watson, says video footage shows the Japanese crew shot themselves in the face with capsicum spray.

"The injuries were self-inflicted by the Japanese, they actually tried to hit our crew with canisters of pepper spray," he said.

"And the video we have shows them firing the spray into the wind and it blowing back on them and them holding their eyes. So they actually shot themselves in their faces with pepper spray.

"So what Japan has done is they've taken advantage of the fact that they have three crew members with self-inflicted injuries, and then they've turned the blame on us.

"And I've asked for an apology from the fisheries minister, who said he was absolutely outraged about our behaviour. Well we're quite outraged that they're blatantly lying about this."

There have been two major clashes between Sea Shepherd and whaling vessels this year.

On January 6 the Sea Shepherd's speedboat Ady Gil was sliced in two by a whaling vessel, and just last week the group claimed its ship the Bob Barker was intentionally rammed.