An increase in ocean temperatures to the east of New Zealand may impact several local fish species, NIWA says.
The National Institute of Water and Atmospheric Research (NIWA) said since 2006, strong, full-depth ocean warming has occurred south of the Chatham Islands at around five times the global rate due to ocean currents moving 120km west.
The water that sits along the Chatham Rise is known as the Subtropical Front.
It is where cold, fresh water from the Southern Ocean met the warm, salty water from the subtropics.
"Over the years, it has gone through periods of warming and cooling," NIWA physical oceanographer Dr Phil Sutton said. But he said it had always come back to baseline.
"However, since 2006, an area south of Chatham Islands started warming and hasn't stopped, and models predict this will continue until beyond 2100," Sutton said.
NIWA used satellites and Argo floats - robotic instruments that move up and down through the water column and drift with the ocean currents - to test the water.
They found that areas that once contained cooler, fresher water were now warmer and saltier.
Global climate models predicted that this system-wide change would strengthen and persist until at least the end of this century.
NIWA principal scientist for fisheries Dr Matt Dunn said several local species were likely to be affected by the temperature change.
"It's a change that is unprecedented really. Changes like this have happened in other countries, but it's the first time that we've seen something like this in New Zealand."
Dunn continued: "There are animals adapted to live on the warm northern side and others adapted to the cold southern side, so when warm waters encroach, you'd expect the species that favour the warmer conditions to increase, and those that favour cold conditions to move away or disappear," he said.
"However, it might take a few years, or a few fish generations, for the scale of the changes to become clear," Dunn said.
Dunn told Midday Report the Subtropical Front was not expected to move and the changes were unexpected.
"The reason we have our big fisheries there is because of this meeting of the water that produces this highly productive zone."
Those fisheries include hoki and orange roughy.
According to MPI, over 200,000 tonnes of fish are caught from New Zealand's deepwater fisheries each year.