Doc staff discovered the bloody body of 11-month-old female sea lion Rua near Quarantine Point, north of the Portobello Marine Aquarium, on Saturday.
A member of the public had reported seeing the lifeless animal to Doc.
The sea lion, born last summer at Warrington Beach, had a bullet hole on her left side near her flipper, and a deep gash on her right side.
Doc Coastal Otago ranger Jim Fyfe said the sea lion's death was ``devastating''.
``We put a lot of work into community relations around sea lions.''
Doc coastal Otago operations manager Annie Wallace said Rua was one of 11 sea lion pups born on or near the peninsula last summer.
``The brutal senseless shooting of a defenceless threatened animal is a tragedy ...
``The impact of her death on the recovery of the New Zealand sea lion is not to be underestimated.''
The New Zealand sea lion - population about 10,000 - is on the highly critical list.
Rua was last sighted at Allans Beach, on the peninsula, in September.
The area in which the sea lion was found indicated she had been shot by someone in a boat, Mr Fyfe said.
``It is a bit strange, but as we've seen before, it does happen.''
Rua's body was sent to Massey University yesterday for a necropsy to determine the cause of death.
New Zealand Sea Lion Trust trustee Amelia Saxby condemned the killing.
``We hope those who carried out this reprehensible act are found and face the harshest penalty.''
The incident raised questions about the whereabouts of other sea lions, Mr Fyfe said.
``There are six females that should be around, that aren't.
``What's the chances of finding a shot sea lion if it is well hidden?
``This has just raised the question of how rife this is,'' he said.
Doc and police were investigating.
Sea lion pup Rua at Warrington back in January.
