The Parliamentary Commissioner for the Environment has recommended that the commercial catching of native longfin eels be suspended to stop the species slow decline to extinction.
Jan Wright says the Department of Conservation (DoC) has failed to protect this species of eel, despite categorising it as at risk and declining.
About 140 tonnes of longfin eel is caught each year.
In a report tabled in Parliament on Wednesday afternoon, Dr Wright says these 50-million-year old predators have suffered greatly from hydro dams blocking their path to breeding grounds, polluted rivers poisoning them, as well as commercial and customary fishing.
To stop the decline, she wants the commercial catching of longfin eels suspended, increased protection for the species and an expert review of the eels' status.
Dr Wright's report attacks the Ministry for Primary Industries' management of the eels, saying its science doesn't add up.
The risk of extinction has been dismissed by the ministry, which overrules DoC on eel management because it is a fished species.
A spokesperson for the commercial eel industry says it is not true that the species is at risk of becoming extinct and there is no need to close the commercial fishery to allow it to recover.
Bill Chisholm says its decline has been largely caused by the construction of hydro dams, which destroyed the ability of about 6000 tonnes of the eel to reach breeding grounds.
He believes Dr Wright is taking the soft option by calling for the industry to be closed down, and instead should focus on improving the quality of the eel's habitat.
Mr Chisholm says about a third of the longfin eel population is protected in national parks and conservation areas.
In a joint statement, the Ministry for Primary Industries and the Department of Conservation say their staff are looking at the report's recommendations.
Maori trust seeks urgent study
A trust representing Maori interests in freshwater fisheries is calling for urgent studies on the decline of the longfin eel which it says has an annual economic value of $10 million.
Te Wai Maori chairman Ken Mair says the minister needs to urgently review the information provided by Dr Wright.
Mr Mair says given the long-term and ongoing significance of this species for Maori, the review should include their expertise.
He says it is an issue of national significance and should be reflected in the reform of freshwater management.
Mr Mair says habitat restoration is key to the survival of longfin eel.
He says drainage of swamps for farmland and removal of suitable riparian cover and flood plains are the biggest problem for longfin eel survival.
Mr Mair says commercial eelers could also be contributing to the slow collapse of the fishery and he is calling on all parties to be part of a remedy solution.
He says cultural value of the longfin tuna is just as important to Maori as the economic value of the eel.
Kahungunu ki Wairarapa environmental manager Rawiri Smith says suspending commercial harvesting of longfin eels or tuna makes good sense, until there is evidence that numbers are healthy.
He says longfin tunas are breeding in Tonga and Fiji at present and when they migrate back to New Zealand again, it will be possible to get a better idea of stock numbers.
