New Zealand is missing crucial opportunities to manage its vast marine estate - for the simple reason that we know too little about it, researchers say.

In a new paper, scientists surveyed the country's research community to pinpoint 90 questions that studies should be trying to answer now.

"Ninety-six per cent of New Zealand is actually in the sea, but our marine environment is at risk and we need to get organised to meet the challenges ahead," said one of the paper's authors, Dr Rebecca Jarvis of Auckland University of Technology.

"At worst, we run the risk of not knowing enough to be able to halt environmental decline or mitigate the dangers that threaten our ocean, and the plants and animals that live there."

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Jarvis described our current knowledge of our marine estate - stretching to 4.4 million sq km, the world's largest - as being patchy at best.

Although around 80 per cent of New Zealand's flora and fauna could be found in the sea, scientists had only identified less than one quarter of the species they believed live there.

"Scientists are, on average, discovering seven new marine species every fortnight, which is faster than we can even name and classify them," she said.

"High resolution maps of our seafloor are lacking, and we are still very much in the discovery phase in New Zealand."

We also weren't entirely sure what the future of the oceans would even look like - or how this would affect Kiwis, Jarvis said.

"There are numerous efforts currently underway which are revolutionising the way in which marine science is done in New Zealand, leading to rapid knowledge advances," she said.

"But there is still so much we need to know."

The paper narrowed down 10 key questions across nine areas: fisheries and aquaculture, biosecurity, climate change, marine reserves and protected areas, ecosystems and biodiversity, policy and decision-making, marine guardianship, coastal and ocean processes, and other anthropogenic factors.

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Those questions ranged from what impact ocean acidification would have on marine resources, and where and how should we set up more marine protected areas, to how trawling and dredging could be affecting productivity on continental shelves, and how we could pick up "tipping points" in ocean ecosystems before it was too late.

"We'd like researchers to pursue these questions, and we'd like decision-makers and funders to use them as a framework for developing new policy and funding opportunities to pursue these important areas of research," said co-author Dr Tim Young, also of AUT.

"Ultimately, targeted research to answer the questions identified by the paper will bridge existing knowledge gaps that can make the greatest contributions to marine science, policy and management.

"Our marine environment is vulnerable and at risk, and we need to work together to protect it and meet the challenges ahead."