Growing demand for omega-3 health supplements is leaving Antarctic waters short of krill, according to a marine conservation group that is blaming Australian manufacturer Blackmores.

But the supplements giant insists it sources the tiny crustaceans, which are a staple food for some whales, using only certified methods.

Sea Shepherd Australia on Thursday launched a campaign targeting Blackmores over their manufacture of pills, EcoKrill, for which it's claimed factory ships are vacuuming the ocean of krill.

With stocks having already been impacted by climate change and ocean acidification, leading to a reduction of some 80 per cent since the 1970s, Sea Shepherd director Jeff Hansen says Blackmores is one of the main offenders.


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

"We must stop the devastation being wrought at the bottom of the food chain or face severe consequences, including a dramatic collapse in fish populations, penguin numbers and dire impacts on whales."

Mr Hansen said treatments containing krill oil are the latest "superstar" in Australia's multi-billion dollar health supplement industry and that Blackmores is one of the nation's largest producers, controlling about 20 per cent of the market.

He called on the company to find an alternative for omega-3.

But Blackmores boss Christine Holgate said the data used to underpin Sea Shepherd's argument is different to that supplied by governing authorities, adding that the company uses only krill sourced in a sustainable way, as certified by the Marine Stewardship Council.

"Not only do we rely on their methods and monitoring, we also have sent our own sourcing manager to observe the catch and ensure we are comfortable that it is fished within the (official) quota and guidelines," she said.

"To our knowledge we're the only Australian brand with a krill product working with these certifications."

Sea Shepherd has asked Blackmores to shift their catch out of Antarctic waters so as not to threaten the whales of the Southern Ocean.