The Ministry for Primary Industries (MPI) is facing fresh criticism for being too close to the fishing industry, amid debate over protection measures for the New Zealand sea lion.
Submissions to the sea lion threat management plan closed on Friday, but scientists and environmentalists say a major threat to the rare mammal, squid fishing, isn't addressed.
"The Ministry for Primary Industries is very close to the fishing industry and often acts as an advocate for them, and yet they also have role of managing species like the sea lion," Forest and Bird's Kevin Hackwell says.
"That is a conflict of interest."
The Department of Conservation (DoC) says bacterial disease Klebsiella is the top threat to sea lions, while many drown after they're tangled in squid fishing nets.
MPI faced criticism last month over a failure to act on commercial fishers' underreporting of endangered dolphins, with the World Wildlife Fund calling for an independent investigation.
The squid fishing industry's permitted a "kill quota" each season of 68 sea lions, and has developed "SLEDs" or sea lion exclusion devices to reduce sea lion bycatch.
But Otago University scientist Bruce Robertson says there's not enough evidence to prove sea lions aren't killed or injured by the devices then washed out of the nets, preventing their bodies from being counted in the quota.
"Unfortunately what happens is the Government assumes that sea lions that get out of nets are in tip top condition and that 95 percent of them will survive. Where that number comes from is quite controversial."
He says the Government's threat management plan started with good intentions, but the process is flawed.
"We [scientists] can review the science then it gets passed on to the fishery managers in MPI, then the scientists are told to get stuffed."
Non-profit Deepwater Group which represents New Zealand's deepwater fishing sector denies the accusation that the industry's too close with the ministry.
A spokesperson for the group says its goal is to not catch sea lions and "we take every practical step, based on good management practice and science advice to achieve this".
They said there were no reported sea lion deaths in the squid season this year and 92 percent of the fishing effort was audited by Government observers.
Mr Hackwell says the "kill quota" doesn't take into account that it's often pregnant mothers hunting for food that are caught in nets, so her death also results in the death of her unborn pup and the pup she's left on shore.
He says the threat management plan doesn't deal with the impact of fishing.
"We're saying you can still fish for squid, there are techniques like jigging that are perfectly safe for sea lions."
A 2013 expert panel review of squid fishery sea lion bycatch shows carcasses brought on board trawlers had declined substantially, but there was still uncertainty around whether some animals were killed but their bodies washed out of the nets.
It also said testing estimated a low risk of head injuries from impact with SLEDs, but could not resolve where some sea lions were drowned but not recovered.
One of the Government's principles for managing biodiversity is to take a precautionary approach, meaning conservation shouldn't be postponed because of a lack of knowledge.
Mr Hackwell says it's failing to take this approach, which equates to gambling with our endangered species.
"We shouldn't wait for evidence of irreversible harm before we take action."
He says there's no independent input in the regulation of threats to sea lions, and MPI's too cosy with the fishing industry.
"The MPI and the industry are hand in glove on how they manage sustainability of the fishery.
"They're [MPI] completely conflicted when it comes to looking after the public interest."
MPI director of fisheries management Dave Turner says the threat management plan's made up of the best available scientific information.
"Submissions to the consultation…have come from a broad cross-section of contributors which will all be considered as part of the review process."
DoC says there are roughly 10,000 New Zealand sea lions left on the planet, some on the Otago coast and most in the sub-antarctic Islands.
It's estimated pup numbers saw a 50 percent decline between 1998 and 2009, which resulted in conservation and MPI officials developing a threat management plan to work out what's killing them.