There are fresh concerns about the fate of the critically-endangered New Zealand sea lion, with disease found to have struck down Dunedin's latest arrival.

The Department of Conservation has confirmed a two-week-old young female sea lion died from klebsiella, a disease that affects the heart and lungs.

Massey University was unable to determine what caused the pup, born to female sea lion Gem, to get sick.

"Deaths of females of critically endangered species is never good news," said DOC coastal ranger Jim Fyfe.

However, the worry was increased by the fact that disease was something new in the Dunedin sea lion population.

New Zealand Sea Lion Trust scientist Shaun McConkey said young sea lions dying from disease was something new.

"We've not really had any problems with disease before. It's obviously affecting our young and really going to slow the population.

"If anything the population is going backwards."

Fyfe said it was a major concern what caused the young mammal to contract the disease.

It was also a concern that more than one pup had died in the past 18 months.

"We've had single pups die before but this is the first year we've had more than one die."

McConkey recently criticised reports there could be a local population explosion of the protected sea lion, saying the current situation was "tenuous".

Residents could not be confident the population would stay stable, he said. Whether the population continued to increase was also debatable.

The New Zealand sea lion, also known as the hooker sea lion, is classified nationally critical, the highest category of threat to endangered species.

- D Scene

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