The 6m strap-toothed whale, a species of beaked whale, was believed to have died at sea sometime in the past couple of days.
A Dunedin woman witnessed it being washed ashore on the incoming tide about 8.30am and contacted the Department of Conservation.
Local iwi were consulted, after which staff from Doc and the University of Otago's Department of Marine Sciences examined the carcass.
Doc acting area manager for coastal Otago David Agnew said the whale's head was cut off for further scientific analysis.
The remains were to be buried early today.
Mr Agnew said it was not uncommon for strap-toothed whales to wash ashore, having died at sea.
"We probably get two or three every year around Dunedin," he said.
The species preferred deep water and spent little time on the surface.
Dunedin's coastline was a likely spot for such whales to wash ashore, because the ocean was relatively deep not far from land.
Some whales died after being hit by ships or propellers while on the water's surface and others died naturally.
The female found yesterday had a torn jaw and a hole in its side, which may have been where birds or fish had fed after it died.
Unlike other whales, strap-toothed whales did not have prized teeth or bones, he said.
They were found throughout the Southern Ocean and were not endangered.
