Otago Regional Council biodiversity senior scientist Scott Jarvie said as many as 88% of those regionally endemic species were identified as having heightened risks of extinction.
The council had "statutory obligations to protect" those species, Dr Jarvie said.
The list of species endemic to the region should be treated as preliminary, but his report would provide evidence to support biodiversity management across Otago, he said.
There were "lesser known taxonomic groups" such as fungi, freshwater invertebrates and spiders not included in the present list.
And of the 360 species identified as endemic to the region, only 194, or about 54%, had been assessed nationally for their threat status.
Otago was home to 25 nationally critical species, 15 nationally endangered species and six nationally vulnerable species, he said.
The most numerous species group of "regional endemics" was invertebrates, with 302 species, he said.
Indigenous vascular plants followed with 40 species.
There were nine regionally endemic freshwater fish, six reptiles found nowhere else on the planet and two bryophytes (mosses and liverworts) — as well as the Otago shag.
The fossil record and archaeological midden analysis found the large shags were once spread widely along the east coast of the South Island but after human arrival they became restricted to rocky cliffs and islands off Otago’s coast.
"Such specialisations often make them susceptible to the effects of environmental disturbances."
The regionally endemic species list would soon be cross-referenced with a recently completed Climate Change Vulnerability Assessment for terrestrial organisms, he said.
Councillors will consider the report at today’s science and resilience committee meeting.
