An adult female and a young pup were found dead with large gunshot wounds to their heads at Ohau Point, north of Kaikoura, on Saturday, in a "grotesque" act that has outraged DOC.
Now, DOC and police are appealing for witnesses or anyone with information on either slaying to come forward.
DOC's biodiversity programme manager on Stewart Island Brent Beaven says there is nothing to suggest the two shootings are linked, apart from the fact "they both involve senseless killings".
"We take all deliberate attacks on marine mammals seriously and, wherever possible, prosecute anyone found responsible," he said.
The sea lion, which is a critically endangered species only found in New Zealand, would have suffered for some time before it died.
"There are only around 10,000 of them left and their numbers are declining," Mr Beaven said.
"As the weekend seal shootings in Kaikoura have highlighted, we need the public to help us safeguard vulnerable marine mammal species."
New Zealand sea lions used to breed from Cape Reinga to Stewart Island.
Their remaining breeding stronghold is now limited to the New Zealand subantarctic islands, with the only mainland locations where they are known to breed in small numbers being Stewart Island, the Catlins and Otago.
"An additional frustration for us is that we were following the female's movements around Rakiura using satellite tracking equipment only two months before it was shot," Mr Beaven said.
"We have now lost any further information it could have provided to help us understand where the animals feed and travel in order that we can better protect the species. This was a sad and needless death."
Seals are protected under the Marine Mammals Protection Act 1978 and anyone caught killing or harming them can face six months in jail or a $250,000 fine.
In 2010, 23 seals were bashed to death with a metal bar at the same location.
Renwick man Jason Godsiff was convicted for killing the mammals and initially sentenced to two years' imprisonment.
However, this was reduced to eight months' home detention on appeal.
Also in July 2010, Hayden John Ingram, of Kaikoura, was fined $500 and sentenced to 200 hours' community work for shooting a seal with a paintball gun, bashing it with a metal bar and running over a seal pup, killing both.
In 2008, Harley McKenzie was jailed for four months for his role in an attack on a leopard seal in which fist-sized stones were thrown at the seal and it was dragged around a beach by its tail.
In 2005, All Black Andrew Hore and friends Hamish Wilson and Matthew O'Connell were each fined $2500 after they shot at seals, killing one, on the Otago coast.
Anyone with information about the Stewart Island incident, should phone police or 0800 DOC HOT (0800 362 468), or for the Kaikoura killings, contact DoC on (03) 572-9100 or Kaikoura police on (03) 319 5038.
