The pup and her mother, Jade, made headlines in February when they were discovered on a Tuapeka farm.
Their discovery so far up the Clutha River was "new, unexpected and exciting behaviour" for the species.
But last month the pup was found dead after being shot and apparently left to die a slow and painful death.
On Tuesday, a Catlins local found the decomposing body of Jade about 100m from where her pup's body was found.
Doc Southern South Island Operations Director Aaron Fleming says shooting a sea lion was an appalling thing to do and staff were sickened.
“Sea lions are a protected species and it’s a very serious offence to intentionally injure or kill one.
“It goes without saying these kinds of incidents must stop. Most people will be deeply disgusted by this sort of behaviour against a protected species and the DOC team is genuinely shocked.
“It’s a tragedy both mother and pup have been shot. DOC staff are determined to find the person responsible and urging the public to contribute any information which may help the investigation.
“We want to find the person who has done this so they can be held accountable. Anyone with any information is asked to come forward by calling 0800 DOC HOT (0800 362 468).”
Jade was well known to the local community and her loss is devastating for locals and those who work with the species, Mr Aaron Fleming said.
“We don’t know when, where or why these sea lions have been shot, or if they were shot at the same time. Any information could help.”
A local vet performed an x-ray and examination, which found about 50 shotgun pellets. Some of these will be forensically tested to see if they match the pellets found in her pup.
“She was lying down and facing away from the shooter, with most pellets entering her chest and spine.”
It’s another major setback for the species’ Southland population, where only seven pups were born this year.
Sea lions began breeding in the Catlins again in 2006 and today there are just 12 breeding age females in the local area.
The NZ Sea Lion Trust is offering a $6000 reward for information leading to a successful prosecution.
Co-chair Shaun McConkey described the death as a "devastating loss to a small population that has only recently returned to the area".
“It's important to remember these sea lions are taking fish to feed themselves and their young not just for recreation or enjoyment.
“Thanks to generous donations from the public the reward has increased to a maximum of $6000 for any and all information leading to a successful prosecution in regard to these recent sea lion killings. Please visit our website www.sealiontrust.org.nz for further details.”
Under the Wildlife Act, it is illegal to injure or kill protected native wildlife like sea lions and anyone who does so can face punishments of up to two years imprisonment and/or a fine of up to $250,000.
