A Department of Conservation plan allocating commercial fishing funding for marine research has fallen short of the expectations of both scientists and fishing interests.
Doc has released its conservation services annual plan for 2013-14 after consultation with those involved in marine science and commercial fishing.
Its objectives were to understand the extent of adverse effects from commercial fishing on protected species and develop solutions to remedy those effects.
To do that observers were to be placed on fishing boats around New Zealand.
University of Otago Assoc Prof Liz Slooten said the amount of observer coverage had improved on previous years, but the reasons behind why some areas received more coverage than others were still unclear.
''There is a definitive improvement in 20% in observer days, but it's such a long way from a scientifically credible observer programme.''
She had asked Doc about three times to clarify the decisions, but it had not, she said.
''It's disappointing. These decisions often appear to be political, rather than scientific, and that seems to be the case here.''
Some coverage decisions were yet to be confirmed, so she hoped that instead of putting observers on board, Doc would ban gill net and trawling from those areas as part of a management plan due out.
Seafood New Zealand chief executive Tim Pankhurst said the seafood industry had many long-standing concerns about the programme, including the lack of a comprehensive and integrated plan to guide conservation services projects, other Doc research and related Ministry of Primary Industry (MPI) research.
''In the absence of such a plan, Doc's CSP projects tend to represent a pretty ad hoc collection from one year to the next.''
There was a lack of public funding for the monitoring of protected species populations, and as a result this monitoring often happened only if Doc or the MPI believed it could attribute the costs of the work to the fishing industry, he said.
''Work of this nature often gets batted back and forward between Doc and MPI, without a good assessment of the proportion of the costs that are properly cost-recoverable.
''There is an opportunity here for public-private partnerships for funding this type of research on a voluntary basis, bypassing some of the issues around whether the costs are legitimately recoverable,'' he said.
Doc marine species and threats manager Ian Angus, of Wellington, said Doc's research on marine mammals and seabirds was not restricted to the conservation services plan.
''You can't look at the CSP in isolation as it doesn't capture the breadth of the work we're doing.''
There was also research being done by Doc and the MPI as well as universities and Niwa. Doc and the MPI planned their research together each year, he said.
Doc and the MPI last year decided to revisit its strategic plan to look at priorities and develop a more collaborative process with the MPI, nongovernmental organisations and the fishing industry, he said.
''We're hoping to finalise that in the next fortnight.''
New Zealand was the seabird capital of the world and on a major highway for marine mammals, many of which were protected, he said.
''If we wanted to [to protect them all] we'd need funds the size of the health budget, but that's not feasible.''