It is not clear if the injuries it sustained were due to natural causes or human-inflicted.
The small population of sea lions on the Catlins coast suffered a significant blow last month when a dead female sea lion, known as Jade, was found riddled with shotgun pellets in the area just weeks after her young pup was shot and killed nearby.
Department of Conservation (Doc) Murihiku operations manager John McCarroll said at this stage the sea lion’s injuries were not linked to the recent shooting deaths of Jade and her pup.
"We will know more once the necropsy results are available.
"The sea lion was not tagged, and we were unable to confirm whether it is one of the 12 breeding-age female sea lions known to us in the Catlins or not."
Members of the public notified Doc and the New Zealand Sea Lion Trust of a female sea lion found injured near Waipati Estuary in the Catlins early last week, he said.
It had two "puncture wounds" near its shoulder and had lost the use of its left flipper.
"We were unable to tell the cause of these injuries, they may be from a natural cause," Mr McCarroll said.
Due to the severity of the injury, and the remote location where it was found, vets recommended euthanasia "which was undertaken humanely via lethal injection on Friday".
"We are very grateful for the help we received from the NZ Sea Lion Trust and Dunedin Wildlife Hospital."
Dunedin Wildlife Hospital Trust manager Jordana Whyte said she hoped Doc would expedite the necropsy.
"Just because the sooner we get information — if it turns out it was human-inflicted — the faster the response, the better if there’s going to be an investigation."
However, she said she hoped the sea lion’s death was due to natural causes.
The puncture wounds were "unspecific" and it was possible a big male had "gone for her, bitten her".
The female that died was only about 2 years old, and small, and due to the significant size difference between young females and larger males it was possible its wounds were inflicted by a male.
"We just don’t know."
Nevertheless, it remained "very concerning" there had been a third female sea lion killed in the Catlins in a matter of weeks considering the marine mammal’s low numbers in the area.
"It’s devastating," she said.
"That’s a pretty big hit to a very small breeding population."
Yesterday, a Doc spokeswoman said the department could not provide an update on the death of Jade and her pup.
Investigations continued, she said.
