The footprints were found in the remote Sierra de Tarahumara mountains in the northern state of Chihuahua, the Institute said.
The prints belong to three adults -- only one of them left impressions of both feet -- and a child about four years old.
The ancient inhabitants likely lived in caves in the Ahuatos valley, some eight kilometers (five miles) from the town of Creel, the Institute said.
A local resident informed the researchers of the find.
"It took us a lot of work to find them because they are not easily identified," said anthropologist Jose Concepcion Jimenez.
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While no other footprints were found, experts found nearby the remains of primitive camps dating from the Pleistocene Era (1.8 million to 10,000 years ago), the statement read.