Researcher Brian Foerster initally thought the discovery would not fit into the “known evolutionary tree”.
The Paracas skulls were discovered on the desert peninsula of Paracas, on the southern coast of Peru, by native archaeologist Julio Tello in 1928.
In 2015, discussing earlier DNA tests on the remains, he said: “The mitochondrial DNA (from the mother) presented mutations unknown to any man, primate or any other animal and the mutations suggested we are dealing with a completely new human-like being, very distant from Homo sapiens, Neanderthals or Denisovans.
“I am not sure it will even fit into the known evolutionary tree.”
Research by sceptics later uncovered that those involved had a history of involvement and belief in research into paranormal subjects such as the Yeti and so-called alien hybrids, an alleged cross breed between humans and aliens.
Sceptics argue the skulls are just another example of intentional cranial deformation, as seen among many ancient South American tribes.
Now Mr Foerster, who is director of the Paracas History Museum, has released details of DNA tests he said were carried out in conjunction with the Peruvian Government and he appears to now accept they were probably human in origin.
In two video updates about the DNA, Mr Foerster made no mention of extraterrestrials.
He described how the Paracas skulls appeared to share DNA links with other elongated skulls found between the Black Sea and the Caspian Sea.
Mr Foerster believes the elongation is not just caused by artificial cranial deformation, but rather by genetics with some of the elongated skulls cranial volume being up to 25 per cent larger and 60 per cent heavier than conventional human skulls.
He says this means that they could not have been intentionally deformed through head binding or flattening, as cranial deformation can change the shape but does not alter the volume or weight of a skull.
Speaking at the Elongated Skulls Symposium in Los Angeles, Mr Foerster said: “What it does show for sure is that the Paracas elongated skull people were not 100 per cent Native American.
“They were a mix or even you could say, in some ways, a hybrid of different people.
“Their blood types are very complicated as well, they should be blood type O if they’re 100 percent Native American and that’s not the case.
“We are likely looking at a sub-species of humanity as regards to the Paracas. It seems to be a lot of DNA evidence from extreme eastern Europe and extreme western Asia.
“More specifically I’m talking about the area in between the Black Sea and the Caspian Sea where ancient elongated skull people lived I think about 3,000 years ago.
“So I think we are looking at a migration pattern starting in the Caspian Black Sea area and then entering through the Persian Gulf and then moving eastwards eventually winding up on the coast of Peru.”
He added: “It appears that the largest elongated skulls on the planet have been found, A in Paracas, Peru and B in the Caucasus area in between the Black Sea and the Caspian Sea.
“So my theory is that there was a sub-species of human which we are going to be eventually calling Homo-Sapiens-Sapiens-Paracas, and they were living in the area in between the Caspian and Black Sea.
“They were invaded by somebody and so they were forced to flee.”
Archaelogist Mr Tello found more than 300 of the odd skeletal remains in a complex grave system in 1928.
Scientists say it was the most extreme example of skull elongation, a deformation practice carried out by several ancient cultures by binding infants heads through pieces of wood, ever found.
Many conspiracy theorists remain convinced they must have been the skulls of visiting aliens.
According to a report on the Conspiracy Club website the previous DNA results were amazing.
It said: “A recent DNA analysis performed on some of these skulls has presented amazing results that could challenge the current perspective of the human evolutionary tree.
“Since their craniums (Paracas) are 25 percent larger and 60 percent heavier than regular human skulls, researchers strongly believe that they couldn’t have been modified through binding.
“They are also structurally different and only have one parietal plate as opposed to the two normally found in human skulls.
“These differences have deepened the decade-old mystery around the Paracas skulls and researchers haven’t been able to explain their origins.
“The implications of this discovery are huge. Who were the mysterious Paracas people?
“Did they evolve here on Earth on a path so different from us that they ended up looking drastically different?”