The historic find was made close to the Guatemalan border in an area plagued with violent smuggling gangs.
Investigators thought the decapitated skulls were unfortunate victims of ruthless local gangsters and launched a probe to uncover how the remains got there, the Daily Star reports.
After 10 years of extensive tests, experts learned the women were not murder victims, but human sacrifices beheaded during rituals to the Aztec gods millenia ago.
A spokesperson for INAH, the Mexican National Institute of Anthropology and History, said: “Believing they were looking at a crime scene, investigators collected the bones and started examining them in Tuxtla Gutierrez”, the state capital.
Experts have said the unfortunate victims had been beheaded and their skulls put on display in a trophy rack known as a “tzompantli”.
It is believed were killed between 900 and 1200CE.
What confused investigators is that pre-Hispanic skull piles usually show a hole knocked through each side of the skull and are found in plazas not caves.
Among the vicitms of this latest find there were more women than men, with none of them having any teeth.
In the wake of the find, archaeologist Javier Montes de Paz said people should probably call archaeologists, not police.
“When people find something that could be in an archaeological context, don’t touch it and notify local authorities or directly the INAH,” he said.
In 2017, archaeologists found a staggering 650 skulls caked in lime at the Templo Mayor, one of the main temples in the Atzec capital Tenochtitlan – which went on to become Mexico City.
They also found thousands of skull fragments encased in the same central edifice.
A few years later, Mexican archaeologists found the remains of over 100 Aztec men, women and children who were suspected to have been sacrificed to the gods.
The grisly findings were discovered during the restoration of a building in Mexico City and are believed to be part of a five metre “skull rack” at a shrine to the Aztec god of the sun, war and human sacrifice.
Hundreds of human heads have been previously unearthed at the site, first uncovered three years ago.