The Southern Ocean has surprised scientists by increasing its capacity to absorb carbon dioxide emissions, but they are warning it could come at a cost to marine life.

About a quarter of the world's carbon emissions are absorbed into the ocean each year, with 40 per cent of that going into the Southern Ocean.

Ten years ago the ocean's ability to absorb CO2 began to decline, meaning emissions were instead being absorbed into the atmosphere.

A report published in the journal Science today shows the Southern Ocean carbon reservoir, or "sink", has since increased, but scientists warn it will lead to further ocean acidification.

CSIRO and Antarctic Climate and Ecosystems CRC scientist Bronte Tilbrook, who collaborated with scientists from America and Europe on the research, said the sink had increased again by about 0.6 billion tonnes of carbon per year — about six times Australia's emissions.

"What it's shown is while the sink did weaken in the 1990s, it looks like it's coming back since about 2002," he said.

"So it's returning to the levels that we expect, which is a big relief."

"It means that the Southern Ocean is continuing to take up large amounts of carbon dioxide, but there is a concern there's a lot more variability than we understood.

"So it's not clear that that sink will continue, it could revert back to lower values, we just don't know."

Dr Tilbrook said the changes in the sink are believed to be caused by changes in the weather.

"Wind and weather patterns around the Antarctic are having a big impact on the variability of the sink," he said.

"Predictions now are that there's a big El Nino coming so it's really important for us to understand how the Southern Ocean sink is changing."

He warned of growing levels of acidification caused when carbon dioxide dissolves in salt water.

"The changes we expect to see in ocean acidification in this century are likely to be bigger than anything these marine organisms have seen in the ocean for the last 20 million years," he said.

"We're changing the system really dramatically.

"The problem with ocean acidification is that a lot of the organisms in the Southern Ocean, and even in tropical systems including coral reefs, are going to have trouble growing shells and skeletal material.

"They're taking energy from normal life processes like growing and defending themselves against viruses and diseases to growing their shells and skeleton."

Dr Tilbrook said ocean acidification also affects the metabolic and physiological processes inside organisms including development, growth, reproduction and respiration.

"What we're doing is putting stress on parts of the ecosystem that will have flow-on effects that we don't really understand," he said.

"It's a major concern for the future of marine ecosystems."