One would cover 1267sq km – about 14 per cent of the forum's region – and include six "no-take" MPAs and a further five "Type 2" MPAs, where restrictions were placed on certain types of fishing.
This network would also ban commercial harvesting of bladder kelp north of the Otago Peninsula, and covered 18 of the 22 coastal habitats found within the forum region.
The second option was much smaller and covered 366 sq km, or 4.1 per cent of the region, with three no-take MPAs, two Type 2 MPAs, and coverage of 10 of the 22 coastal habitats.
The first and larger option was backed by environment, tourism, community and science representatives, as well as one of the two recreational fishing representatives.
The second smaller one was supported by the commercial fishing representatives and the forum's third recreational fishing representative.
The ministers would now work through the next steps, which involved consultation with colleagues and agencies.
It wasn't yet clear what steps would be needed if new marine protections were required.
Before any changes are made to existing protections, they would seek the views of all parties in Parliament and invite public submissions.
Nash said the forum members had been given a challenging task, and had spent "a great deal of time" looking at how to protect marine environments.
Some fishing representatives had asked for more work to be done but Nash said that wasn't necessary.
"We are happy with the quality of the report and the robust and demanding process followed by the forum.
Sage said MPAs were vital to protect important habitats and feeding areas for marine mammals, birds, fish and invertebrates.
"New Zealand's marine environment is 15 times larger than its land mass and it's important this is safeguarded for future generations," she said.
Forum chair Maree Baker Galloway said the three-year process had required groups to reach consensus on "very testing issues".
"There's been tension between different sectors and the process has involved many heated but constructive debates," she said.
"Eventually the forum members reached agreement on what recommendations would be presented to the ministers and collectively deserve to take pride in their achievement."
But Forest & Bird argued the proposals still fell short, as no marine reserves were offered in the southern third of the ocean area and many habitat types received no protection at all.
"Severely threatened species such as hoiho/yellow-eyed penguins are on a knife-edge; they are being caught as fishing industry bykill, and threatened by climate change and warming seas," the group's marine advocate Anton van Helden said.
"I think New Zealanders will be horrified that we've missed this opportunity to safeguard our ocean environment for future generations.
"If we want to save such iconic species we need to do more."
The group pointed out the forum's terms of reference included establishing an ecologically representative and well connected system of MPAs, and argued neither of the two recommended networks met that requirement as both protected less than 5 per cent of the area as marine reserves.
"If the forum can't meet its objectives after three-and-a-half years of work, then the process is flawed," van Helden said.
"The forum clearly bent over backwards to cater to existing users like the fishing industry – although ironically, the science is clear that marine reserves increase fish stocks.
"All the proposals are second best – the best canyon isn't protected, nor are the best areas for biodiversity.
"Public submissions and science overwhelmingly supported more protection – especially in terms of extending protection from the shore right out to the 12-nautical-mile limit."
"We are calling on the Government to implement the largest amount of protection recommended by the forum.
"But the Government also needs to urgently work with stakeholders to ensure the terms of reference are met and marine reserves are created in the southern third of the area."
The sentiments were also echoed by Otago University marine biologists.
Professor Phil Seddon, of the university's Department of Zoology, said the forum should be applauded for its efforts in what was a highly contentious area.
But he added that neither of the two recommendations would do much to address the South Island's glaring lack of MPAs.
"Pocket-handkerchief sized fragments of isolated protection will do little to assist the wide-ranging and iconic native seabirds such as hoiho, the yellow-eyed penguin, whose populations along the Otago coast continue to decline due to multiple factors, including fisheries-related habitat degradation and by-catch," Seddon said.
"Some hard decisions need to be made around whether we prioritise sustaining marginal economic activities, or conserve our dwindling and irreplaceable natural heritage."
Professor Liz Slooten also called the report "very disappointing".
Scientists had overwhelmingly asked for larger protected areas, buffer zones and better protection for mobile species including marine mammals, yellow-eyed penguins and other seabirds, Slooten said, but the two proposals were based largely on "social compromise rather than science".
"Given that the group was dominated by extractive users of the marine environment, the result was pretty predictable.
"This problem is well recognised, with similar expert criticism of the water forum as well.
"This kind of stakeholder group tends to result in the lowest common denominator, with the environment losing out almost every time."
