The gas comes mainly from living organisms, prompting some to believe that life of Mars could after all exist.
The latest findings from NASA's Curiosity rover, which has been exploring the red planet since it landed in 2012, were published in the US journal Science and raise the question of whether microbes could be the source of the methane.
Organic chemicals in soil samples collected by a drill of the rover were also found.
While the discovery of life on Mars would be a major breakthrough, NASA's John Grotzinger cautioned that the findings need more investigation.
However, he said the discovery was "really exciting news" because "it is the kind of material that you would look for if life ever originated on Mars."
"We now have full confidence that there is methane occasionally present in the atmosphere of Mars," he said.
The methane and the organic molecules from a rock-powder sample collected by rover's drill "can both be consistent with the former presence of life or the existing presence of life," Grotzinger said.
Curiosity is not equipped to find out whether life currently exists on Mars, but the mission aims to uncover whether life ever arose there by looking for chemical elements that are the building blocks of life, including carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.
