The girl's family voluntarily submitted a DNA sample to police after she was spotted several times in Queenstown, New Zealand, in March and then again New Years Eve by a retailer who became suspicious by the resemblance she bore to McCann.
Police sent the sample to Scotland Yard, which confirmed that the DNA did not match that of the missing girl, New Zealand media reported.
"We have received confirmation from Scotland Yard that a DNA sample provided voluntarily from a girl mistaken as missing British girl Madeleine McCann on New Year's Eve in Queenstown last year does not provide a match for that of the missing girl," said Detective Inspector Steve McGregor of the New Zealand southern police.
"At the time of the sighting police made thorough inquiries and were completely satisfied that the girl was not Madeleine McCann."
The family of the Queenstown girl has requested to remain anonymous.
McCann was just shy of her fourth birthday when she disappeared while on vacation with her parents at the Ocean Club in Praia da Luz, Portugal on May 3, 2007.
Gerry and Kate McCann have pushed continuously to maintain the ongoing worldwide search, sinking more than £1 million from the sales of Kate's bestselling book Madeleine into the search.
The Portuguese police stopped their formal investigation in July 2008, after more than a year of searching had turned up no conclusive evidence. The McCanns were able to get the Metropolitan Police to reopen the investigation 18 months ago.