A juvenile leopard seal has been shot and killed at the at the Ōreti River mouth, near Invercargill.
The Department of Conservation was first alerted to the death of the protected animal on July 23.
It appeared the seal had been shot with a small-calibre rifle, the department said.
"Evidence on site suggests a vehicle had been circling around the animal which may have caused it further distress," a spokesperson said.
"Leopard seals are protected under the Marine Mammals Protection Act 1978 and offences against them carry significant penalties."
Anyone who killed a protected animal could face a maximum sentence of two years in jail or a fine of up to $250,000.
Department of Conservation senior biodiversity ranger Rosalind Cole said, following consultation with the local Waihopai rūnaka, the seal would be allowed to decompose naturally.
"Leopard seals are considered a taonga species to Ngāi Tahu. Local iwi has expressed how sad and tragic it is that a member of the public would carry out such an act on a defenceless marine mammal. We completely agree."
Leopard seals were easily identified by their snake-like appearance, with long slim bodies, disproportionately large heads, massive jaws and impressive teeth, the department said.
They usually dwelled in the Antarctic but visit New Zealand's shores sometimes, usually in autumn and winter.
The juvenile otherwise looked in good health, so it was unclear why it might have come ashore.
The department was appealing for anyone with information about the animal's death to call 0800 362 468 and ask for the Invercargill team.