A report recommends sweeping changes to the recreational fishing sector.
New Zealand's fishing industry could hit a snag if it doesn't plan for warmer oceans significantly affecting marine life, say Niwa scientists.
As the ocean gets warmer it could affect phytoplankton - a key part of the oceans, seas and freshwater basin ecosystems - and could see a reduction in food supply for fish.
"This has already happened in the water just off Tasmania and the south-east corner of Australia, which is warming rapidly as the East Australian current pushes warmer water further south causing huge changes to the ecosystem," said Niwa marine biogeochemist Professor Cliff Law.
Tasmania's coastal ecosystems were changing with an increase in subtropical species, which can impact the economy, he said.
"The average warming around New Zealand is 2.5 degrees [Celsius] by the end of this century, which will affect how the ocean mixes and the nutrients available for plankton growth, with knock-on effects on the foodweb and fisheries.
"People tend to think of climate change from a terrestrial angle but obviously, as the ocean is a big part of the globe, there will be significant changes. As it's also a significant part of New Zealand's Exclusive Economic Zone we need to start planning for this now."
Near-record sea surface temperatures described as "off the charts" were reported on Monday.
A La Nina pattern and higher than normal atmospheric pressure are warming sea surface temperatures by more than 6 degrees Celsius in some areas, compared to the average for this time of year.