Human impacts included high-impact fishing and the expansion of offshore petroleum and minerals exploration, with nutrient pollution and sedimentation from land also having an effect.
On a wider scale, there were dynamics associated with climate change, including warming sea temperatures, rising sea levels, ocean acidification and changes to circulation patterns.
The report characterised the present governance of oceans as a "single sector approach", which attempted to manage the multitude of marine activities and impacts separately, with little capacity to consider interactions or cumulative effects.
"Major users such as fisheries, minerals, aquaculture, science and conservation are managed in relative isolation by different government agencies under different pieces of legislation," the report stated.
"This fragmentation of public policy impedes the development of management systems able to adequately regulate the diverse activities that take place in our seas."
McGuinness Institute chief executive Wendy McGuinness said the present ocean governance framework lacked the vision, principles and capacity for people and groups to share accurate information and develop "meaningful ways forward".
"Intead, decision-makers are left to grapple with difficult and complex issues under urgency and without guidance," she said.
"This has been an on-going problem and it is time to make the system work for the public good. We need to future-proof our economic growth and wellbeing by putting in place a process that informs public, business and policy analysts in an integrated considered way."
If the Government was unwilling to make changes within the present framework, such as creating a Minister of Oceans, a Ministry of Oceans or a Parliamentary Commissioner of Oceans, then Kiwis had to find other ways to progress management, she said.
"We must find a way to explore the management of this asset from a public good perspective and the establishment of a Pacific and Southern Ocean Institute might be one way to bring people together.
"This could include global connections with other countries, such as Russia, China, South Korea, Germany and the US. Put simply, we need to work harder at bringing science and economics together."
In terms of ocean conservation, just under 10 per cent of our territorial sea, or waters within 12 nautical miles of the coast, is now protected by marine reserves - close to the target recommended by the UN.
But when compared against territorial sea and all 4.4 million sq km of our EEZ, just 0.4 per cent is covered by protected areas, although any commercial activities beyond fishing are still subject to environmental regulations under the recently updated EEZ Act.
Just under a third of the EEZ was also covered by benthic protection areas, where bottom trawling and dredging is banned, while 2.5 per cent of our territorial waters are partially protected under another classification applying to cases such as cable and pipeline zones and area-based fisheries restrictions.
By comparison, around a third of our land fell within some form of protected area.
The Government plans to increase protection by reforming the Marine Reserves Act, extending the ability to create marine reserves out into the EEZ, and to allow creation of seabed protection areas, species sanctuaries, and recreational fishing parks.
Two parks already identified would cover areas of the inner Hauraki Gulf and the Marlborough Sounds.
