The leopard seal was found on the Tiwai peninsula, near Bluff, on Tuesday and an investigation was launched, a spokesperson said.
Doc senior ranger biodiversity Rosalind Cole said it was "gutting" that someone would shoot one of the marine mammals.
"It's always heartbreaking when protected species are harmed or killed, but having them deliberately shot is a completely incomprehensible, senseless act."
Leopard seals, which primarily inhabit the Antarctic sea, were "occasional visitors" to New Zealand waters, she said.
"People need to remember that beaches are shared spaces with wildlife. Marine mammals such as seals, sea lions and occasionally leopard seals can and do visit our Southland beaches regularly. Keep your distance, be respectful and keep your dogs under control."
The mammals are protected under the Marine Mammals Act, and anyone harming them could face up to two years' imprisonment or fines of up to $250,000.
The death comes just weeks after a young fur seal was killed by a dog in Invercargill.
Doc urged anyone with information about the death of the leopard seal to contact it on 03211-2400.
