However, Department of Conversation (DoC), in a TMP background document published in June, said although 100 sea lions were being caught a year by commercial trawlers 15 years ago, "the number had declined significantly".
This decline comes from area-based measures, codes of best practice, individual vessel management plans but, most importantly, to sea lion exclusion devices (Sled).
The Sled is designed to allow small species, like squid, to become trapped in the net, but prevents sea lions from entering the end of the trawl net by allowing them to break free through an escape hole.
Ministry for Primary Industries considers about 82 per cent of sea lions survive their interaction with fishing vessels.
Despite DoC's measures Dr Nic Rawlence, who carried out the study, said: "What our research shows is that human harvesting and sea lions do not mix."
Since 1998 sea lion pup births have declined by 50 per cent, and with only about 10,000 sea lions left, the population is in a serious decline.
The New Zealand sea lion is the only native sea lion, and while once could be found all over the country, their breeding sites are now limited to Auckland Islands, Campbell Island as well as smaller breeding sites on Otago and Stewart Island.
The researchers used ancient DNA analysis, radiocarbon dating and computational modelling to analyse the prehistoric population and to understand why the population suddenly went extinct.
"Unless measures are taken to mitigate continuing bycatch levels, the outlook for our sea lions is bleak" said Rawlence.