Methane hydrate, dubbed "burning ice," is methane gas trapped or dissolved in ice formed in deep-sea sediments.
Japan's Ministry of Economy, Trade and Industry said gas was obtained Tuesday from a layer 1,083 feet below a 3,281-foot-deep section of the floor of the Pacific Ocean.
Japan Oil, Gas and Metals National Corp., commissioned by the ministry, first drilled a well to the methane hydrate layer in February and March last year. Final preparations for extracting gas started this past January.
JOGMEC plans to extract thousands to tens of thousands of cubic meters of gas over the coming weeks.
Waters around Japan are estimated to hold enough methane hydrate to produce as much natural gas as Japan consumes in 100 years, Asahi Shimbun reports.
"Gas hydrates have always been seen as a potentially vast energy source, but the question was, 'How do we extract gas from under the ocean?'" Ryo Matsumoto, a professor in geology at Meiji University in Tokyo who has led research into Japan's hydrate deposits, told The New York Times.
"Now we've cleared one big hurdle."
Ryo Minami, director of the oil and gas division at Japan's Agency for Natural Resources, likened methane hydrate's potential to shale gas, which is transforming the U.S. energy market.
"Ten years ago, everybody knew there was shale gas in the ground, but to extract it was too costly. Yet now it's commercialized," he was quoted as saying by the Financial Times.
The "burning ice" extraction announcement comes a day after the second anniversary of Japan's massive earthquake and tsunami, which crippled the Fukushima nuclear power plant.
Prior to the disaster, nuclear plants generated about one-third of the country's electricity. Now only two of Japan's 50 operable nuclear reactors are online, following shutdowns ordered after the Fukushima crisis.
Resource-poor Japan is the world's largest buyer of liquefied natural gas, imported a record 87.3 million metric tons in 2012, an increase of 11.2 percent year on year.
Japan says it hopes to begin commercial extraction from its methane hydrate fields within five years.
That could have a huge effect on Australia's LNG sector. Japan buys 70 percent of Australia's LNG exports, totaling $11 billion in 2010-11 and on course to soar to $30 billion in 2016-17, The Australian newspaper reports.
Wood Mackenzie, in its Horizons 2013 outlook released last December, said that if production of Japan's methane hydrates could be achieved by 2018 it would "reposition Japan on the world energy stage, potentially turning it from a gas importer, to a self-sufficient province."