The skulls, found in Peru, created waves in 2014 after a geneticist undertook preliminary DNA tests, and reported unknown results.
He found they had mitochondrial DNA “with mutations unknown in any human, primate, or animal known so far”.
A second round of DNA tests have now been carried out – which some saying the results are just as controversial – leading to further speculation the skull’s former owners may not have been from this planet.
Elongated skulls were caused by ancient civilisations purposefully mutilating their skulls from a young age.
It was done by binding the head between two pieces of wood, or binding in cloth.
But, they have always interested alien conspiracy theorists due to the enlarged craniums produced, which appear similar to the mythological alien grey species.
The new tests on the skulls have, however, not aided the alien theory, but have raised new questions about how the Americas were populated.
Samples were taken from hair and bone powder, taken drilling deep into a skull’s foramen magnum.
They were then sent to three labs in Canada, and two in the US, for tests.
Geneticists were told the samples were from an ancient mummy, to avoid any preconceptions.
The skulls were now found to have European and Middle Eastern Origin, raising questions over when man first travelled from Eurasia to the Americas, as they are 2,000 to 3,000 years old.
Paracas is a desert peninsula in Pisco Province on the south coast of Peru.
Around 300 of the amazing skulls were found by Peruvian archaeologist Julio Tello in 1928 in an elaborate graveyard.
But there still remains a mystery over the shape of the Paracas skulls.
Cranial deformation changed the shape of a skull, but in normal cases did not alter other features.
However, the Paracas skulls have other unusual features and are the biggest elongated skulls ever found.
Author and researcher LA Marzulli told Ancient Origins: “There is a possibility that it might have been cradle headboarded, but the reason why I don’t think so is because the position of the foramen magnum is back towards the rear of the skull.
“A normal foramen magnum would be closer to the jaw line.”
He said an archaeologist has written a paper about his study of the position of the foramen magnum.
He added: “The archaeologist states that the Paracas skulls, the position of the foramen magnum is completely different than a normal human being, it is also smaller, which lends itself to our theory that this is not cradle headboarding, this is genetic.”
Mr Marzulli claimed some of the Paracas skulls also have very pronounced cheek bones, different eye sockets and no connective tissue joint between the two parietal bones of the skull.
There is a disease known as craniosynostosis, which results in the fusing together of the two parietal plates, however, Mr Marzulli said there is no evidence of this disease in the Paracas skulls.
He stopped short of suggesting they were of alien origin, but the mystery of exactly where they came from looks set to continue.