It aimed to halt their decline within the next five years and to build towards a stable or growing population within the next 20 years.
The plan included more research into the disease Klebsiella pneumoniae, and more planks to stop the animals falling into holes.
But environmental groups criticised it for failing to address what they considered a major threat to the species - commercial fishing - and now researchers argue they have the evidence to provide a direct link.
In their study, just published in the international journal PNAS, the researchers from the University of Otago, Massey University and the University of Toronto analysed Government data to investigate the role commercial fishing has played in the near 50 per cent decline of the species.
They concluded that, despite measures introduced since 2001 to stop sea lions from being killed in fishing nets, commercial fishing continued to affect their numbers.
The authors believe the management of sea lion bycatch in the arrow squid fishery around the Auckland Islands placed the population at risk of extinction, because the Government assumed fishing was not a major threat.
"Several threats, such as disease and fisheries bycatch, have been postulated as causes of the sea lion decline," said lead author Dr Stefan Meyer, a population ecologist based at the University of Otago.
"However, until this research, studies have been unable to link these threats to the decline."
While the observed bycatch had declined since sea lion exclusion devices (SLEDs) were introduced on vessels in the arrow squid fishery, study co-author Associate Professor Bruce Robertson, also of Otago, argued there was no firm evidence to show they'd successfully removed the bycatch threat.
"What information is available raises concerns that the devices may be hiding sea-lion deaths by allowing dead sea lions to fall out of the nets at sea or causing injury that reduces life expectancy or reproductive ability."
Added Meyer: "We now know that sea lion exclusion devices have, despite all assumptions, obscured bycatch of New Zealand sea lions and that this factor posed a significant and ongoing impact to the population.
"Our findings are therefore a game changer in New Zealand sea lion management."
The researchers questioned what they argued was a downplaying of the role of commercial fishing in the sea-lion decline.
"The PNAS study shows that the impact from the squid fishery is likely a key driver of the NZ sea lion decline," Robertson said.
"With fishing threats being ignored in sea-lion management, it is hard to see how the Government's goals to increase the population will be achieved.
"We hope that our study will lead to meaningful management.
"The good news is there are a range of options open to the Government to reduce the impact of fishing on the sea-lion population, while still allowing commercial fishing in the New Zealand subantarctic."
Industry group Seafood New Zealand has rejected the findings.
"The seafood industry refutes the findings of this vague and contradictory report which is peppered with assumptions about the efficacy of sea lion exclusion devices," a spokeswoman told the Herald.
The Ministry for Primary Industries (MPI) had recently reviewed the main squid fishery, SQUID 6T, and concluded fishing was not the major factor of the observed population change, and that the population appeared to be stabilising, the spokeswoman said.
Further, the most recent Aquatic Environment and Biodiversity Annual Report stated that the TMP recognised no single threat was affecting the population, and that recovery would require mitigation of multiple threats at the four main breeding sites, she said.
Three sea lion deaths were attributed to commercial fishing this season. Last year, with 92 per cent observer coverage, no deaths were recorded.
The spokeswoman referred to a 2015 study by two Australian researchers, published in response to earlier work by the same authors of the latest study, and which suggested future work may be "better focused on alternative research and management areas" as "fisheries bycatch has been reduced to levels that are unlikely to be driving continued decline".
"The industry continues to engage best practice to mitigate sea lion captures through the use of SLEDs, the regular training of crew on how to identify the risks, and observers on board trawl vessels," the spokeswoman said.
"The industry also continues to support DoC's conservation work around sea lions in the sub-Antarctic.
"This year's census of sea lion pups showed an increase of 14 per cent."
MPI was completing a technical review of the new paper, and could not comment on its conclusions, a spokesperson said.
"MPI periodically reviews the measures used to manage sea lion interactions with the Auckland Islands squid trawl fishery, and has recently completed public consultation on measures that will be applied in the 2018 fishing season," the spokesperson said.
"Once we have reviewed this paper in more detail, any information that is relevant will be factored into this review."
