WWF-New Zealand spokesperson Alex Smith said that was "out of step" with what the poll had shown.
"Leaving out 95 per cent of New Zealand oceans from proposed legislation aimed at looking after our oceans makes no sense at all."
Smith accused the Government of going back on commitments to allow protected areas in deep oceans.
"The Government needs to listen to New Zealanders and include the EEZ in the new marine protection legislation. It is not too late for common sense to prevail."
Labour and the Green Party back the view.
"The 12-mile limit is an arbitrary line and it's a bit absurd to have one set of rules inside that and another outside it," Labour's environment spokesperson David Parker said.
"There's a need for spatial planning in both sides of the line and therefore the legislation that only speaks to the territorial sea is inadequate."
Green Party environment spokesperson Eugenie Sage claimed industry interests had been put before ocean protection.
"We need to create deep sea marine protection zones to help guarantee healthy fish stocks for future generations, and protect the biodiversity of marine life - including whales, dolphins, sharks, fish, and seabirds."
Fishing industry lobby Deepwater Group told the Herald it supported MPAs, noting around 31 per cent of the EEZ had been closed by law to bottom contact fishing gear since 2007.
"We are open to discussions on options to extend the current restrictions in other MPAs to include other industries," its chief executive George Clement said.
"Our main concerns centre on having an effective MPA policy that both considers the risks to marine biodiversity and is directed at reducing these, and gives due recognition to the existing rights, for both industry and for Maori."
The oil and gas lobby, Petroleum Exploration and Production Association New Zealand (PEPANZ), is against the legislation covering the EEZ, something its chief executive Cameron Madgwick said was like using a "regulatory sledgehammer to crack a nut".
Environment Minister Nick Smith said while there was strong support for the reform generally, points of detail like the EEZ issue had triggered a large number of submissions.
"The Government will take on board the submissions, but we just haven't made a decision at this point in response to them."
Matters around the far-off EEZ were "quite a different scenario" to local communities having input around issues involving the territorial sea.
"The Government has always said it is open-minded about further protection in the Exclusive Economic Zone; it's only a question of whether it is done by way of special legislation, or whether it's done through the new MPA Act."
Our Exclusive Economic Zone
• Covers more than 4.4 million sq km, making it the fourth largest in the world.
• Inhabited by more than 15,000 marine species, with a further 50,000 possibly yet to be found.
• Just 0.4 per cent of it is covered by protected areas, but still subject to environmental regulations under the recently updated EEZ Act.
The survey question
The Government is proposing new legislation to enable a network of marine reserves to be created in New Zealand's seas.
Under this proposed legislation, marine reserves could be set up in New Zealand's coastal waters (out to 12 nautical miles) but not in the deep oceans (from 12 to 200 nautical miles).
The coastal waters make up five per cent of New Zealand's marine environment, while the deep oceans make up 95 per cent.
Do you support or oppose New Zealand's deep oceans also being included in the legislation for marine reserves?
The survey results
*1150 respondents answered with either definitely support, probably support, probably oppose, definitely oppose, or not sure.
*Seventy-six per cent were in support, and those in definite support included Wellington residents, NZ European people and those in higher income households.
*Twelve per cent were in opposition, and those more likely to oppose it included those over 60, those who were retired, and those who identified as Maori.
