About 8 teragrams (8 million metric tons) of the greenhouse gas is leaking yearly from the East Siberian Arctic Shelf, researchers said in the journal Science.
It's unclear whether the seabed has always been leaking, undetected, or whether this is a new development, however.
Subsea permafrost is losing its ability to be an impermeable cap, said Natalia Shakhova, a scientist at the University of Fairbanks, Alaska, and co-leader of the article said.
Scientists say methane is 25 times more potent than carbon dioxide as a global warming gas.
While the team said the leakage doesn't alarmingly alter estimates for global emissions, it may be a precursor to larger venting of the gas.
If it further destabilizes, the methane emissions may not be teragrams, it would be significantly larger, Shakhova said.
The United Nations Intergovernmental Panel on Climate Change in 2007 estimated some 582 teragrams of methane are emitted yearly.
The atmospheric concentration of the gas in 2008 rose to a record 1,797 molecules per billion molecules of air, the UN's World Meteorological Organization said Nov. 24.