Noble experiment
The researchers used noble gases to trace the path of methane as these inert chemicals are not affected by microbial activity or oxidation.
By measuring the ratios of the noble materials to the methane they were able to accurately determine the distance to the likely source.
The scientists analysed content from 113 wells in the Marcellus shale in Pennsylvania and 20 in the Barnett shale in Texas. They found eight clusters of wells with problems.
"The mechanism of contamination looks to be well integrity," said one of the authors, Prof Robert Jackson from Stanford University.
"In about half the cases we believe the contamination came from poor cementing and in the other half it came from well casings that leaked."
Cement is used in the oil and gas extraction industry to fill the spaces between the well casing and the sides of the well.
In one case the methane was linked to the failure of an underground well. In none of the investigated wells was there a direct link to fracking.