The greatest threat to native fauna remained that from introduced animals such as stoats and rats, and changes in climate would also shift the distribution of pests and predators.
DOC backed 1080 poison, calling it a "contentious" pest control tool but the one that remained the most cost-effective one available for possums and rats.
"Its use allows the management of predators across whole landscapes and is vital in the control of bovine tuberculosis (TB)."
DOC's 1080-led "Battle for our Birds" programme, launched to combat a plague of stoats and rodents triggered by a bumper year in the fruiting of beech trees, had the potential to be "transformational" for conservation, the report said.
DOC's highest priority for fresh water would be to protect wetlands of of international importance listed under the Ramsar Convention on Wetlands, and rivers with "high conservation value".
The $20 million Living Waters partnership with Fonterra was "essential" to advancing this.
Some river catchments in stewardship land had been flagged to be reclassified because of high conservation value.
These included the St James Station areas in the Hope River catchment, Canterbury, the Mokihinui River catchment south of the Buller River Scenic Reserve and Te Wahipounamu, a World Heritage Site in the south west corner of the South Island.
The New Zealand Conservation Authority had also recommended that a new national park be established at Northland's Waipoua Forest, the home to giant kauri Tane Mahuta.
The authority had recommended that the support of Te Roroa be obtained before the proposal was progressed, and work with the iwi had already began, the briefing said.
Marine protection, another priority area, could be improved by a legislation overhaul earlier suggested by the previous minister, Nick Smith.
There were still "significant marine ecosystems" that were not within marine protected areas, yet there was no provision for marine areas in New Zealand's Exclusive Economic Zone and the present Marine Reserves Act did not allow for "effective collaborative planning".
"Development of new marine protection legislation would address limitation in the Marine Reserves Act 1971, remove the need to use area-specific legislation and duplicate consultation to protect an area formally once the work of a forum has been accepted by the Government."