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The Department of Conservation released its conservation services programme plan recently, outlining the observer programme for New Zealand's commercial fisheries for 2014-15.
University of Otago marine scientist Liz Slooten said the increase in observer days by 77 to 2487 made for an ''ineffective observer programme''.
''What needs to happen in the inshore fishery is that number needs to be doubled or trebled.''
Added to that was the shift of observer hours from one fishery to another, and in some cases to fisheries that had no impact on Maui's or Hector's dolphins, such as on the west coast of the North Island, she said.
There appeared to be no clear rationale for the move or for why some fisheries were observed 25% of the time and others 65% of the time, she said.
For the trawl fishery on the east coast of the North Island, only 25% observer coverage was planned, yet there was less protection for the dolphins from the fishery in that area.
''It's really urgent we find out the impact on dolphins and sea lions in the inshore trawl fisheries.''
The Government did not appear to be listening to its scientists' advice, which stated they could not establish an accurate estimate of dolphin by-catch in those areas because of a lack of information, she said.
However, the east and south coasts of the South Island benefited from these changes, with observers to monitor penguin interactions 65% of the time along the east coast set net fishery and 100% of the time in the small inshore fishery.
Yellow-eyed Penguin Trust field officer Dave McFarlane was pleased with the observer coverage assigned to Otago's yellow-eyed penguin foraging and breeding areas along the coast from Waitaki to Slope Point, and from Stewart Island to Fiordland.
The trust had been saying for many years more information was needed on set-net fishing impacts on penguins as the population declined and faced challenges related to the sea such as starvation.
''These are not helped by by-catch. There is a clear need for this,'' he said.
Ministry for Primary Industries inshore fisheries manager Steve Halley said coverage decisions were informed by many processes, including previous observer data, ministerial decisions and available risk assessments, the nature of the fishing activity, potential overlap with the protected species and the likely risk of an interaction occurring.
For Maui's dolphins, ministerial decisions informed observer coverage, including mandatory observer coverage on commercial set-net vessels around Taranaki and an increase in observer coverage of the trawl fishery on the west coast of the North Island from 25% in the first year to 100% in four years' time, Mr Halley said.