The trapped organic material that created the gases was a relic of life that teemed in Antarctica 35 million years ago, study co-author Slawek Tulaczyk said.
"Our modelling shows that over millions of years, microbes may have turned this old organic carbon into methane.
"Our study highlights the need for continued scientific exploration of remote sub-ice environments in Antarctica, because they may have far greater impact on earth's climate system than we have appreciated in the past."
Victoria University associate professor of physical geography Jim Renwick said: "Methane is the more powerful greenhouse gas - it doesn't stay in the atmosphere anywhere near as long as carbon dioxide, but while it's there it does a pretty effective job of absorbing heat from the earth.
"If a lot of methane did suddenly get released into the atmosphere, it would have a large effect," he told the Herald.
Separate findings at the opposite end of the globe have signalled warming is happening at an alarmingly fast rate.
New analysis found Arctic sea ice had melted to the lowest extent seen in records that began more than 30 years ago, breaking the previous record low observed five years ago.
Dr Renwick described a rapid melt rate at the start of the month, where an area nearly the size of New Zealand disappeared each day, as "just jaw-dropping".
"This event unfolding in the Arctic Ocean right now should be a wake-up call to governments worldwide that climate change is a serious threat, and it is not [a] distant menace, it is on our doorstep today."
WHAT LIES BENEATH
* Scientists estimate half of the West Antarctic ice sheet and a quarter of the East Antarctic ice sheet overlie pre-glacial sedimentary basins containing about 21,000 billion tonnes of organic carbon.
* They also calculate that the potential amount of frozen methane and free methane gas beneath the Antarctic ice sheet could be up to 4 billion tonnes.
* It would take 196,000 years for the Hampton Downs landfill to generate the same amount of methane.
* Methane release during episodes of ice-sheet collapse could accelerate global climate change.
* Nasa research over 20 years found snow is continually melting across Antarctica - in recent years as far as 800km inland and on mountains two kilometres above sea level.
* Scientists also found that melting had increased on the Ross Ice Shelf, both in terms of the geographic area affected and the duration of increased melting across affected areas.