Dozens of police chased up the report on New Year's Eve.
But today, Detective Sergeant Brian Cameron of Queenstown police said they had identified the young girl seen in Queenstown on were "absolutely satisfied" that she was not the missing schoolgirl.
He declined to release any details of the identified child, stating only that this was not the first occasion that someone had contacted police remarking on the similarity between the two girls.
The woman who reported the sighting told the Southland Times a girl resembling Madeleine entered her store with a dark-haired man late in the afternoon on December 31.
She said the girl had the same eye defect as Madeleine - a coloboma of the iris - in the same eye as the missing Leicester girl.
The woman contacted police and also a 24-hour Find Madeleine hotline. British police have been in contact with the woman.
"My only reason for alerting anybody is because if my little girl was missing and if someone on the other side of the world was seen who bore any considerable resemblance, I would want it ruled out," she told the paper.
Madeleine was 3 years old when she went missing from a resort in Praia da Luz, Portugal on May 3, 2007, while holidaying with her family.
The possible sighting of Madeleine in Queenstown is not the first in New Zealand. In 2010 there were suspected sightings in Dunedin, Milton, Alexandra and Queenstown.