Microplastics are found in three of every four of New Zealand’s fish, huge portions of indigenous seabirds and marine species are threatened with extinction, and warmer oceans are becoming uninhabitable to native species, a stark new government report on the state of the country’s oceans has found.

The ministry of environment’s marine stocktake, released on Thursday, lays out a grim picture of species under threat. It found that 90% of indigenous seabirds, 82% of indigenous shorebirds, 81% of assessed marine invertebrate species and 22% of marine mammal species were classified as threatened with extinction or at risk of becoming threatened with extinction.

More than 4,100 seabirds were killed by longline fisheries in a year, and warmer, more acidic oceans were becoming uninhabitable for taonga (treasured) species and affecting traditional food sources for Māori. The report’s data shows ocean acidification rose 8.6% between 1998 and 2020, overall water temperatures were rising, and marine heatwaves were becoming more frequent and severe.

“The report is right to say it paints a sobering picture,” said the environment minister, David Parker. He pointed to the emissions reduction plan, ban on single-use plastic bags, and freshwater management plans as examples of government action to relieve some of the pressure on ocean environments.

On some measures in the report, things were either improving or staying the same: in nationwide measures for nutrient pollution in the form of nitrogen and phosphorus, more sites had improving trends than worsening trends.

Green party spokesperson Eugenie Sage, however, said the report “tells a decades-long story of government neglect when it comes to the health of our oceans”.

“The health of our oceans is deteriorating at an alarming rate and we’re at risk of losing precious habitats for ever,” she said, calling for greater regulation of the fishing industry, a ban on more single-use plastics and the expansion of ocean sanctuaries.

Conservation group Forest and Bird called the findings a “crisis” and said in a statement that the “true scale of the crisis affecting the oceans could be much worse because the extinction risks facing most marine mammals, fish, and invertebrates remains unknown, due to lack of research”.

“Aotearoa New Zealand is an island nation … we depend on the health of our ocean ecosystems,” said Nicola Toki, Forest and Bird chief executive. “The fishing industry is already suffering the effects of degraded and warming oceans, with dying salmon stocks, and collapsed hoki and crayfish populations.”

Toki called for urgent, cross-party political action “to give our ocean the protection it deserves.”