The juvenile humpback was found at a remote beach at Omini in late July.
There it stayed until about two weeks ago, when large waves took the carcass back out to sea.
Local conservationists were jumping for joy to see it leave, but the celebrations were shortlived.
Two days later, on September 9, the creature rode the morning swells and landed at Purakaunui Beach.
Department of Conservation (Doc) biodiversity ranger Jim Fyfe said the whale had been laid to rest in a shallow grave among the dunes.
The morning after it returned he organised for a pair of contractors to bury it with a 13-tonne digger.
When it first arrived the humpback weighed about 10 tonnes, but it was little more than a "blubbery sleeve" after months of decay.
It decomposed much more rapidly than first expected and lost about half its mass.
The beach was not a popular spot, but those who did use it would struggle to find any sign of the burial.
The remains of the whale would not attract any more predators than a dead seal or sewage waste, he said.
Having the whale exposed to the air brought a variety of problems, such as people trespassing through private property and disturbing the carcass without permission.
There was evidence to suggest pieces of the whale, such as bones, had been taken, which Doc was following up on.
East Otago Taiapure management committee chairman Brendan Flack said the whale had deposited a collection of bones before it was washed out to sea again, which were taken and cleaned for cultural purposes.
People tampering with the carcass were being disrespectful to the whale and to the cultural process, as any permissions had to go through mana whenua, he said.
Now it was buried, the whale could decay without interruption and more bones could be dug up later.
The re-beached carcass was found by Caz Brigham, who was walking around the area.
She thought the corpse was a white rock which had been revealed from beneath the sand. However, she recognised the ridges when she got closer.
It was an incredible find for the curious former biology teacher, but it smelled revolting, she said.
The oil from the whale had leached into the sand and coated her shoes, which had to be soaked in a bleach solution and scrubbed for hours.
Warrington Surf Life Saving Club Club chairwoman Charlotte Becconsall-Ryan said it was fantastic to see the problems bought by the whale finally over.
Although there had been no observed increase in shark activity, the decaying whale brought the risk of predators and had worried locals.
People had been avoiding the area for months.
