Tāiko/black petrels were dying at unsustainable rates due to commercial fishing; kōura/crayfish were classed as functionally extinct, and popular fish species such as snapper and tarakihi remained at concerningly low levels.
Report authors also highlighted the march of the kina barren, due to a depletion of its key prey, crayfish and snapper.
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Minister of Conservation Eugenie Sage said the report showed while there had been some positives above land - in the growth of predator-free islands from 25 to 40 covering 10,000ha - it was a different story at sea.
"In the marine space we need to go much further, much faster. Shorebirds and seabirds are declining, and the impacts of fishing are still far too high."
She also cited the lack of action on marine reserves, with such "no take" areas only increasing by 0.05 per cent in 20 years, covering just 0.3 per cent of the Marine Park.
"There are not enough marine reserves," she said.
The Hauraki Gulf Forum has a goal of protecting at least 20 per cent of the park, with 10 per cent as "no take" marine reserves.
Last year Sage established a ministerial advisorial group to make recommendations on implementing the Sea Change Marine Spatial Plan, released in 2016 to restore the health of the Gulf.
Sage said the group would be looking into expanding marine reserves, along with other protection measures such ahu moana - a tangata whenua/community driven approach, and rāhui.
Recommendations were expected later this year, she said.
Report authors said the legislation that established the marine park needed to be revisited, with the balance tipped too far towards "development and utilisation" over the environment.
Sage said the integrated management the legislation promoted had been effective in some areas, including lowering of boat speeds that had seen the number of Bryde's whales killed drop.
But she agreed it was time for a revisit, although it was not part of the current advisory committee's work.
"In the conflict between economic development and nature, nature has lost out," Sage said.
Dr Shane Kelly, one of the report authors, said a lack of action on protected areas in the marine park in the past 20 years stood out.
"Since the park was established thousands of tonnes have been pulled from the sea, hundreds of hectares in new aquaculture has been consented, millions of cubic metres of storm and diluted wastewater have been discharged, hundreds of new boat berths and boats, yet there is only one new marine reserve, and that application came before 2000."
Forest & Bird's Megan Hubscher said the report highlighted the need for everybody to come together to restore the health of the Gulf.
"It is no secret New Zealand's coastal ecosystems have been trashed through decades of neglect and abuse, and it is no good anymore for different groups to point the finger, to say it is the fault of commercial, of recreational, of land users, of developers - we all contributed to this mess and it is up to all of us to give nature a chance."
She called for urgent enactment of the Sea Change Marine Spatial Plan, and for it to be properly resourced.
Fisheries Minister Stuart Nash said fisheries management in the Hauraki Gulf was an important component of overall collaborative restoration and rebuilding efforts.
"Where stocks are depleted there are rebuilding plans in place and catches have been cut. This includes crayfish, snapper, and tarakihi. For shellfish beds, a new scientific survey of cockle and pipi habitats is under way.
"We are also looking at the ways in which we can better incorporate ecosystem-based fisheries management principals into the way we manage the Hauraki Gulf and the wider fisheries stocks."
