Detective Senior Sergeant Brian Cowie, of Invercargill, said the case of the missing 2-year-old remained open and active.
The bones were unearthed about noon yesterday by contractors excavating part of the Lake Wakatipu foreshore at the end of Churchill St.
Det Snr Sgt Cowie said the contractors notified police, who quickly made their way to the scene.
The site was cordoned off, and as the media gathered and as talk spread that it could be the remains of Amber-Lee, who went missing in 1992, the cordon was expanded further down Churchill St and also extended to include a section of grass reserve.
Det Snr Sgt Cowie said a Queenstown GP viewed the bones yesterday afternoon and believed "they could possibly be human bones".
A large police presence, including detectives from Queenstown and Invercargill, remained at the scene throughout the afternoon, putting on protective clothing and erecting a tent about 50m from where the bones had been found.
As helicopters began to fly over and boats arrived from Queenstown, the mood in the tiny township remained sombre.
Police were notified of her disappearance at 8.15pm on Saturday, October 17 and about 100 volunteers, friends, family and police scoured the area for her.
Two days later, the search was called off and police announced they were treating it as a missing persons case.
Despite various rumours, tip-offs and publicity, Amber-Lee had never been found.
There were hopes yesterday's find might have meant some form of closure for her family.
However, just before 6pm, Det Snr Sgt Cowie announced the bones were "definitely not human".
Pathologist Alex Dempster, of Invercargill, had viewed the bones and came to the conclusion "they are from some sort of animal ... possibly a sheep.
"It's Kingston ... and this is not the first time we've had similar ... finds up here.
We'll treat each one on its merits."
Peter and Margaret Gibson recalled when the 2-year-old first went missing and residents had their water tanks searched for any sign of the little girl, described by police at the time as having "white hair and blue eyes" with a "chubby belly and rosy red cheeks".
Mrs Gibson said she felt "devastated and sick" after she heard through word of mouth that a body had been found yesterday.
Southern District Crime Scene services manager Detective Inspector Steve McGregor, of Dunedin, said speculation yesterday was "understandable ... but this outcome demonstrates why police exercise caution in these kinds of circumstances".
The contractors are putting in a slipway for a new tourism boat, the 60-tonne Pacific Jemm.
It will be launched on Friday.
