Expedition leader Steve Rintoul of Australia said his multinational team of researchers had found that waters at the bottom of the "southern ocean" were significantly cooler and less salty than they were 10 years ago.
The "southern ocean" is in the Antarctic region and was delimited from the southern portions of the Atlantic Ocean, Indian Ocean and Pacific Ocean in 2000 by the International Hydrographic Organisation.
Rintoul said the size and speed of the changes surprised scientists, who have long believed deep ocean waters underwent little temperature change, and could indicate a slowdown in the flow of deep water currents.
"Ocean circulation is a big influence on global climate, so it is critical that we understand why this is happening and why it is happening so quickly," Rintoul said on Thursday, after he and his team docked at Hobart on the Australian island state of Tasmania.
"The surprise was just how rapidly the deepest parts of the ocean are changing, at depths of 4 or 5km below the sea surface," Rintoul said.
"Whether it's a natural cycle that takes place over many decades, or it's climate change, it's an indication that the deep ocean can respond much more rapidly to changes that are happening near the surface than we believed possible," he said.
"The surprise was just how rapidly the deepest parts of the ocean are changing, at depths of four or five kilometres below the sea surface"
Steve Rintoul, expedition leader
The expedition sampled 3000km of the "southern ocean" basin during an eight-week expedition aboard the Australian Antarctic Division's research ship Aurora Australis.
Their findings added urgency to the study of climate change, Rintoul said.
"It's another indication that the climate is capable of changing and is changing now," he said.
"What we need to do is sort out if this is human-induced change and if so, how rapidly is the climate going to change and what will the impacts of that change be?" he said.
The new findings emerged a day after the UN's Kyoto Protocol on climate change came into force. The treaty aims to cut production of so-called greenhouse gases believed responsible for a warming of Earth's climate.
During its expedition, the Australian-led team released 19 free-floating ocean robots known as Argo floats, which are designed to drift with ocean currents to better measure temperature and salinity.
The floats, part of an international ocean-monitoring effort, drift about 2km underwater and surface every 10 days to deliver findings.
Rintoul said the Argos would provide a huge boost to climate research. "They will revolutionise how we understand the ocean, in particular to determining climate change and shorter climate cycles," he said.