The Department of Conservation says the shooting of a young female sea lion in the Caitlins will affect the population growth of the vulnerable species, which has been slowly recovering in recent years.
It is seeking information from the public after the juvenile sea lion, pakake, was found dead with injuries consistent with being shot.
DoC Murihiku operations manager John McCarroll said staff received reports of a distressed sea lion in the Catlins estuary on Monday morning.
When a ranger went out to investigate, they found the young female had died.
He said shooting a protected sea lion was a disgusting act that was completely unacceptable.
"The sea lion had serious injuries to its hindquarters which look to have been caused by a firearm, and steel shot believed to be from a shotgun cartridge was recovered from the animal."
He said DoC staff were appalled someone could have shot the sea lion and left it to die a slow, painful death and wanted to find out who was responsible.
It is illegal to injure or kill protected native wildlife - with a penalty of two years imprisonment and/or a fine of up to $250,000.
"We don't know where, when or why the sea lion was shot. They are mobile animals and this juvenile had been seen around wider Catlins Estuary area and up the Clutha River Mata-au earlier this year.
"Our best guess is the sea lion has been bearing these painful injuries for over a week, which would have affected its ability to swim and hunt."
McCarroll said the loss will compromise future population growth in the region.
"There are very few female sea lions in the region so each one is extremely important."
The deceased sea lion is being sent to Massey University for a necropsy to confirm the cause of death.
NZ Sea Lion Trust Co-chair Shaun McConkey said he was extremely disappointed there were people who would commit such an act, especially towards an endemic species that has only recently returned to the mainland after a long absence.
"Our sea lions are charismatic and curious animals that will sometimes approach people, making them particularly vulnerable to anyone that might intend them harm."
He said it was another blow to a small, establishing population that had already experienced low pup survival over the last couple of years.
The sea lion's mother Jade was born under a crib (bach) at Kākā Point in 2016 and was named after the late son of the bach owners.
Pakake have a threat status of nationally vulnerable and number about 12,000. About 96 percent of the population lives in the Subantarctic Islands and is in decline.
On the mainland, there are small but growing populations in Rakiura/Stewart Island, Murihiku/Southland, and Otago.
Anyone with any information is asked to please contact DOC on 0800 DOC HOT (0800 362 468).