Australia's production of omega-3 health supplements is having a devastating impact on krill stocks in Antarctic waters, a marine conservation group says.

Sea Shepherd Australia on Thursday launched a campaign targeting Blackmores over its manufacture of pills, Eco Krill, for which it is claimed factory ships are vacuuming the ocean of krill, a key component of the food chain.

Krill stocks threatened by demand for omega-3, Sea Shepherd claims. Credit:AP

With climate change and ocean acidification having already slashed krill stocks by some 80 per cent in the Antarctic Ocean since the 1970s, a further reduction cannot be sustained, Sea Shepherd director Jeff Hansen said.

"This practice affects the entire Antarctic ecosystem, including penguins, birds, whales, and fish," he said.