This decline came from area-based measures, codes of best practice, individual vessel management plans and, most importantly, sea lion exclusion devices (Sled).
The Sled is designed to allow small species such as squid to become trapped in the net, but allows sea lions to break free. The Ministry for Primary Industries believes about 82 per cent of sea lions survive an encounter with a fishing vessel.
But 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 births have fallen 50 per cent, and with about 10,000 sea lions left, the population is in serious decline.
The New Zealand sea lion is the only native sea lion. While once it could be found all over the country, breeding sites are now limited to the Auckland Islands, Campbell Island and smaller sites in Otago and Stewart Island.
The researchers used ancient DNA analysis, radiocarbon dating and computational modelling to analyse the extinct population and to understand why it suddenly died out.
"Unless measures are taken to mitigate ... by-catch levels, the outlook for our sea lions is bleak," said Rawlence.