DISTRESSING CONTENT: Rua, an 11-month-old female sea lion, has been shot dead on the Otago Peninsula, shocking conservation staff.

Department of Conservation (DOC) staff recovered her body on Saturday, and pleaded for help to find the culprit.

"We have nothing to go on, but we really want to get to the bottom of this," DOC Coastal Otago operations manager Annie Wallace said.

She had a message for the killer: "It would be really nice for us and all those other people who hold these animals dear for us to understand what was going through their head."

The sea lion was found with a puncture wound to her side, consistent with a bullet hole, and a deep cut on the other side of her body.

It was unclear if the deep cut was an exit wound, she said.

Rua's body was sent to the Institute of Veterinary, Animal and Biomedical Sciences at Massey University on Monday morning for a necropsy to determine the cause of her death.

"The brutal senseless shooting of a defenceless threatened native animal is a tragedy."

Rua was one of only 11 sea lion pups born on the peninsula last summer, and "the impact of her death on the recovery of the New Zealand sea lion is not to be underestimated".

"The few female sea lions around Dunedin are precious to the survival of the species," Wallace said.

"Rua was an otherwise completely healthy pup and we have every reason to believe she would have gone on to be a productive breeder."

One of the world's rarest sea lions, New Zealand sea lions had a population of 10,000 and were classified as critically threatened, the same as kakapo and kiwi.

Rua was last seen alive on Allans Beach on the peninsula in September.

Her birth at Warrington Beach last summer prompted the local community to name and care for her.

Police are investigating the incident.

DOC asked anyone with information about Rua's death to contact the Dunedin DOC office on 03 477 0677, the DOC hotline on 0800 362 468 or Dunedin police on 03 471 4800.

It is illegal to injure or kill sea lions and anyone apprehended faces serious penalties, including up to two years' imprisonment and a fine of up to $250,000 under the Marine Mammals Protection Act 1978, and five years' prison and a fine of up to $100,000 under the Animal Welfare Act 1999.