The University of Texas at Austin study, funded mostly by energy interests, says the EPA estimates of "fugitive methane" were fairly accurate but based on 2-year-old data, so they didn't reflect the growing use of emissions-reducing technology.
The new study's data, published in the peer-reviewed journal Proceedings of the National Academy of Sciences, were from 2012.
The "green completions" technology, used by 67 percent of the wells studied, was able to "capture or control 99 percent of the potential emissions," the study says.
The extra equipment, introduced by the EPA last year, will be mandatory for all natural gas wells in January 2015.
At the same time, the UT study found much higher-than-expected gas leakage from pneumatic switches, used to turn equipment on and off at well sites, the authors report, adding this finding should help regulators and the industry further reduce emissions.
The findings support the argument that switching power generation from coal to gas will help reduce the greenhouse-gas emissions believed to contribute to climate change, advocates say.
Methane, natural gas' primary ingredient, is 20 to 100 times more potent as a greenhouse gas than carbon dioxide.
The findings also support the importance of federal regulation of gas production, an issue highly controversial in the industry, environmentalists say.
About 90 percent of the $2.3 million study's funding came from nine oil and gas companies, including Exxon Mobil Corp., Chevron Corp., Royal Dutch Shell PLC, Anadarko Petroleum Corp., Encana Corp. and Pioneer Natural Resources Co. The remaining money came from the Environmental Defense Fund environmental advocacy group.
The study's 14 authors, led by university chemical engineering Professor David T. Allen, declared "no conflict of interest." They said their research was independent and affirmed they controlled the study's design, data collection and analysis.
But The New York Times reported one author, Jennifer Miskimins, has been employed by a petroleum engineering firm since last year.
The university said it would look into Miskimins' possible conflict of interest.
Critics of fracking, or hydraulic fracturing, argue large amounts of methane leak from gas-drilling sites. Some suggest it would be better for the environment to burn coal instead of natural gas.
A 2011 Cornell University study led by ecology and environmental biology Professor Robert Howarth suggested the EPA leak estimates were too low and natural gas production was holding back carbon emissions reductions.
Howarth said in a written response to Monday's study if the findings accurately represent the industry, they suggest natural gas can be produced with "modestly low emissions."
But he said he doubted the findings were representative.
Gas companies "do better when they know they are being carefully watched," he said.
Environmental Defense Fund Chief Scientist Steven Hamburg told the Times gas companies would be hard pressed to speedily clean up their act at fracking sites ahead of the researchers' visits, given the short lead time on choosing well sites. He said procedures and equipment are developed well ahead of time.
Physicians, Scientists & Engineers for Healthy Energy, a group critical of fracking, called the study "fatally flawed" by the small sample size and oil industry influence.
Exxon Mobil said: "This groundbreaking survey -- the most extensive ever conducted -- adds important new evidence demonstrating that hydraulic fracturing does not compound climate change. This is an important step forward and a valuable contribution to our scientific understanding of this matter."
Shell called the study a "validation for regulators," adding "compliance and enforcement will be important."
Fracking is a technique to extract oil and gas from rock by injecting high-pressure mixtures of water, sand or gravel, and chemicals.