Isaac Koi, who specialised in studying UFO film footage, said the magazine's footage was the work of artist John Humphreys who had confirmed he made the alien being, the Mirror reported.
But Eisen told NZME. that he was confident the footage was authentic.
There was nothing in Alien Autopsy that showed the same images, he said.
The clip was studied by a well known Mexican journalist, who Eisen said he was not at liberty to name, but who said the footage was legitimate.
"It has not been analysed by film archivists, Kodak, to the best of my knowledge," he said.
"Alien Autopsy is a rather obvious hoax, I don't think that this is a hoax."