Researchers, examining 30 years of data, said chinstrap and Adelie penguin numbers had been falling since 1986.
Warming waters, less sea-ice cover and more whale and seal numbers was cited as reducing the abundance of krill, the main food source for the penguins.
The findings appear in the Proceedings of the National Academy of Sciences.
Antarctic krill (Euphausia superba) is a shrimp-like creature that reach lengths of about 6cm (2in) and is considered to be one of the most abundant species on the planet, being found in densities of up to 30,000 creatures in a cubic-metre of seawater.
It is also one of the key species in the ecosystems in and around Antarctica, as it is the dominant prey of nearly all vertebrates in the region, including chinstrap and Adelie penguins.
Warming to change
In their paper, a US team of scientists from the National Oceanic and Atmospheric Administration (Noaa) and the Scripps Institution of Oceanography said a number of factors were combining to change the shape of the area's environment.
"The West Antarctic Peninsula (WAP) and adjacent Scotia Sea support abundant wildlife populations, many of which were nearly [wiped out] by humans," they wrote.
"This region is also among the fastest warming areas on the planet, with 5-6C increases in mean winter air temperatures and associated decreases in winter sea-ice cover."
They added that analysis of data gathered during 30 years of field studies, and recent penguin surveys, challenged a leading scientific idea, known as the "sea-ice hypothesis", about how the region's ecosystems was changing.
"(It) proposes that reductions in winter sea-ice have led directly to declines in 'ice-loving' species by decreasing their winter habitat, while populations of 'ice-avoiding' species have increased," they explained.
However, they said that there findings showed that since the mid 1980s there had been a decline in both ice-loving Adelies (Pygoscelis adeliae) and ice-avoiding chinstraps (Pygoscelis antarctica), with both populations falling by up to 50%.
As a result, the researchers favoured a "more robust" hypothesis that penguin population numbers were linked to changes in the abundance of their main food source, krill.
"Linking trends in penguin abundance with trends in krill biomass explains why populations of Adelie and chinstrap penguins increased after competitors (fur seals, baleen whales and some fish) were nearly extirpated in the 19th to mid-20th Centuries, and currently are decreasing in response to climate change," they wrote.
The team said that it was estimated that there was in the region of 150 million tonnes of krill for predators after the global hunting era depleted the world's whale population.
During this period, data shows that there was a five-fold increase in chinstrap and Adelie numbers at breeding sites from the 1930s to the 1970s, they reported.
"The large populations of Adelie and chinstrap penguins were not sustained for long, however, and are now declining precipitously."
They added that this was happening as rising temperatures and decreases in sea-ice was altering the physical conditions required to sustain large krill populations.
"We hypothesise that the amount of krill available to penguins has declined because of the increased competition from recovering whale and fur seal populations, and from bottom-up, climate-driven changes that have altered this ecosystem significantly during the past two to three decades."
The US researchers concluded that the penguin numbers and krill abundance were likely to fall further if the warming trend in the region continued.
They wrote: "These conditions are particularly critical for chinstrap penguins because this species breeds almost exclusively in the WAP and Scotia Sea, where they have sustained declines in excess of 50% throughout their breeding range."
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