Initial evidence suggests she was killed with a shotgun.
Department of Conservation Murihiku operations manager John McCarroll said Doc staff were horrified by the apparent shooting and painful death of the pup in the Catlins estuary.
He said shooting a protected sea lion was a "disgusting act and completely unacceptable", and Doc was calling for the public to come forward with any information about who might have done it.
"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.
"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."
Doc staff were "appalled" someone had seemingly shot the sea lion and left it to die a slow, painful death.
"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.
"We don’t know where, when or why the sea lion was shot.
"They are mobile animals and this juvenile had been seen around the wider Catlins estuary area and up the Clutha River Mata-au earlier this year."
Mr McCarroll said the pup was being sent to Massey University for a necropsy to confirm the cause of death.
New Zealand Sea Lion Trust co-chairman Shaun McConkey was both angry and extremely disappointed to hear about the incident.
"You just want to say to this person: ‘Grow up. These animals aren’t doing any harm. Just live and let live’.
"I thought that we’d got past that sort of behaviour.
"When sea lions first started turning up on our shores, there were quite a few people talking about them being aggressive and that Doc needed to do something about them and they needed to be removed and they didn’t belong here.
"That attitude has definitely changed over the years and a lot of the locals are really embracing the sea lions.
"It’s just a shame that we’ve still got people out there that go out there and do this sort of thing — especially to a very young animal."
Mr McCarroll said the threatened species had only returned to the mainland in recent years, and the loss of the female pup was a huge blow for the recovering population.
"There are very few female sea lions in the region, so each one is extremely important.
"The species is slowly regaining a presence in the South Island after a long absence and we need to do everything we can to foster their recovery ...
people will need to get better at sharing our coasts with sea lions."
The pup and her mother, Jade, made headlines in February when they were discovered on a Tuapeka farm, and Doc coastal Otago biodiversity ranger Jim Fyfe said their discovery so far up the Clutha River was "new, unexpected and exciting behaviour" for the species.
He said pregnant females were known to push inland to escape the attention of males at that time of year, but he never thought they would choose a site so far from the sea.
New Zealand sea lions are classified as nationally vulnerable.
About 96% of the estimated 12,000 animals live on subantarctic islands, but there are also small and growing populations on Stewart Island, Southland and Otago.
Mr McCarroll said it was illegal to injure or kill marine mammals. Anyone who did so could face up to two years’ imprisonment and/or a fine of up to $250,000.
