Environmental groups are urging the government to crack down on commercial industries whose activities are harming the marine environment.
The latest snapshot of the state of our oceans paints - yet again - a bleak picture of what's happening beneath the waves.
The Ministry for the Environment's second marine report released today show the human activity on the land and at sea - such as coastal development and seabed trawling - is devastating marine habitats, with pests and invasive species taking over.
On top of that, the environment is dealing with the impacts of climate change.
Forest and Bird chief executive Kevin Hague said for too long the ocean had been treated like a limitless resource.
"For a hundred years we've treated the ocean as a guilt-free, consequence-free dumping ground for our waste and what we're now seeing is that both of those assumptions were completely wrong."
He said it was time to make serious changes to the status quo.
"The government needs the courage to stand up to the industries which are driving this crisis: urban developers, farming, forestry, shipping, fishing, oil and gas.
"A fundamental shift to the way New Zealand does business is required."
Mr Hague said while some parts of industry were making a genuine effort to change, overall it needed to happen a lot faster.
"We're now reaping the consequences of that laissez-faire attitude."
Greenpeace oceans campaigner Jessica Desmond agreed.
"This report further demonstrates the urgent need for an overhaul of fisheries management if we want to protect our oceans. It shows we can't continue to claim individual fish stocks are sustainable while turning a blind-eye to by-kill and gross habitat destruction.
"As a nation that is fifteen times more ocean than land, we should be embarrassed by how poorly we're looking after our waters. The majority of our native ocean species are threatened, yet we continue to exploit the sea as if this isn't the case."
However Seafood NZ chief executive Tim Pankhurst said the industry was improving on its own.
"The seabird bycatch has halved, to an estimated 4186 seabird deaths in the 2016-17 fishing year, compared to 8192 in the 2002-2003 year."
"We recognise this is still too many and our fishers are making strenuous efforts and adopting innovative technologies on a pathway to the ideal of zero bycatch," he said.
The report said in 2018, 84 percent of routinely assessed stocks were considered to be fished within safe limits, an improvement from 81 percent in 2009.
Of the 16 percent that are considered overfished, nine stocks were collapsed, meaning that closure should be considered to rebuild the stock as quickly as possible.
Mr Pankhurst said a more pressing issue was sedimentation, from land-based activities like urban development, forestry and agriculture.
Environment Secretary Vicky Robertson said the data on fishing showed things were improving.
"There is some good news there. Only 16 percent of our fish stocks are overfished so the rest are looking good. But counting fish stocks doesn't actually tell us much about the habitats around them."
"Dredging and trawling numbers are decreasing and the bycatch numbers are decreasing so that actually is on track for improvement."
Mr Hague said the depletion of some fish species was still very concerning and said Forest and Bird disagreed with the quota that had been allocated for some species.