• Our coasts are the most degraded of all marine areas, due to sediment and nutrients washed off the land, introduced marine pests, and seabed trawling and dredging.
But it found the full ecological impact of fishing "was not clear" - and did not draw firm conclusions about specific effects of commercial, recreational and customary fishing.
Secretary for the Environment Vicky Robertson said our oceans are facing multiple, and cumulative pressures that have been building over generations.
"Our waters have become more acidic from absorbing excess CO2," she said.
"This affects the creatures that live there. Among other things, ocean acidification makes it more difficult for shellfish, like pa and mussels, to form shells."
"Climate change was also warming the ocean and causing sea-level rise, which affected not only on fish but also other wildlife and our own coastal communities.
Some of our marine wildlife and coastal habitats were in a fragile state, she said.
"Ninety percent of our native seabirds and shorebirds are threatened with or at risk of extinction.
"More than a quarter of our native marine mammals are threatened with extinction."
"Fishing by catch, introduced predators, and habitat change are among a raft of reasons for the poor state of much marine wildlife."
But where challenges had been identified, some results were being seen; the number of seabirds caught by commercial fishing by catch almost halved from around 9000 in 2003 to 5,000 in 2013.
While the full picture of fishing pressures was lacking, the report did some include some statistics and data.
In 2015, 17 percent of the New Zealand fish stocks were over fished - meaning they were depleted and needed active management or had collapsed and needed to be closed.
This compared with an estimated 29 percent of fish stocks over fished worldwide.
The status of some fish stocks in the Quota Management System were not known but knowledge of the status of fish stocks making up most of the main commercial species had improved since 2009, the report found.
While the report used the most up-to-date data, Government statistician Liz Macpherson said national data on many marine issues remained limited.
"The environmental reporting programme is working to improve our data over time.
"However, New Zealanders need to consider the costs of delaying action in the absence of perfect information."
It was released alongside a companion paper by Statistics NZ, showing the marine economy contributed 1.9 percent, or $4 billion, to our gross domestic product (GDP) in 2013, about the same as the 2 percent contribution in 2007.
Offshore minerals - mainly oil and gas - were the largest contributor to the marine economy, at $2 billion in 2013.
The three big issues
1. PRESSURES FROM CLIMATE CHANGE ARE GROWING
Ocean acidification may cause widespread harm to New Zealand's marine ecosystems, particularly to marine organisms with carbonate shells like pa, mussels, and oysters, the report found.
Ocean warming may affect ocean currents, modify habitats, and expand or reduce the areas where marine species are found, and is a primary cause of rising sea levels.
New Zealand's Sub-Antarctic waters have become more acidic since measurements were
first made in 1998. This ocean acidification is consistent with changes measured
elsewhere in the world.
Sea-surface temperatures in New Zealand's waters showed a statistically significant
increase of about 0.71C over the period between 1909 and 2009.
Sea levels around New Zealand's coastline had also risen between 1.31 and 2.14 millimetres a year on average since reliable measurements began in 1900, at a rate consistent with sea level rise worldwide.
Ocean acidification and warming would continue for generations.
2. MANY SPECIES ARE THREATENED WITH EXTINCTION
Most of our marine bird species are threatened with or at risk of extinction, including species of albatrosses, penguins, and herons.
More than one-quarter of our marine mammal species are threatened with extinction,
including the New Zealand sea lion and species of dolphins and whales.
Of the 92 indigenous seabird species and subspecies that breed in New Zealand, 32 (35 percent) are classified as threatened with extinction and 51 (55 percent) are at risk of extinction.
Of the 32 species and subspecies threatened with extinction, 12 are nationally critical, facing an extremely high risk of extinction, including species of albatross, shag, petrel, and penguin.
Nine percent (8 of 92) of our indigenous seabird species and subspecies have had an increased risk of extinction since 2008; the risk decreased for only one species over the same period.
Of the 14 indigenous shorebird species and subspecies that breed in New Zealand, eight (57 percent) are classified as threatened with extinction and four (29 percent) are at risk of extinction.
Their fragile state is due to multiple historic and present day pressures, although accidental deaths of seabirds and marine mammals from fishing (bycatch) have decreased.
3. COASTAL MARINE HABITATS AND ECOSYSTEMS ARE DEGRADED
Of all marine environments, our coastal ecosystems are under the most pressure from human activities.
Pressures interact in complex ways to degrade coastal habitats and ecosystems, and impacts can accumulate over decades.
The degradation of coastal habitats undermines their functions in the wider ocean ecosystem and compromises Maori values, commercial activities, and New Zealanders' recreational enjoyment of coastlines and beaches.
The most important coastal pressures, alongside ocean acidification and climate change impacts, are: excess sedimentation, seabed trawling and dredging for fish and shellfish, marine pests and excess nutrients carried down waterways.
Excess sedimentation is caused by activities such as forest harvesting, clearing land for agriculture, and urban subdivision.
Coastal marine habitats such as rocky reefs, sandy beaches, pipi beds, seagrass meadows, and sand and mud flats, are particularly vulnerable to sedimentation.
Heavy metals, from run-off from roads and other sources, are toxic to both animals
and humans even at low concentrations.
Heavy metal concentrations in estuaries and harbours are mostly at levels unlikely to cause harm to seabed species, based on data from 10 regions.
The number of non-indigenous marine species in New Zealand's coastal waters has risen 10 percent since 2010.
Between 2010 and 2015, 33 new non-indigenous species were recorded, of which 12 have established in New Zealand's waters.
Other coastal pressures include other fishing methods, dumping of dredge spoils, reclamation (infilling of harbours and estuaries for coastal development) and pollution from waste water and plastic debris.
