Academics fear for New Zealand's declining sea lion population after discovering a rare breed of sea lion was "rapidly" driven to extinction after contact with humans on the Chatham Islands, in the 17th century.

An international research team, led by Otago University scientists, proved a new type of sea lion existed 650km east of New Zealand's mainland, but was wiped out 200 years after Polynesian settlement of the island in about 1650.

The study indicated that any hunting rate greater than one sea lion killed by one person a year was enough to wipe out an entire population in 200 years, and the study added to growing evidence that undetected bycatch may be behind the declining sea lion levels in New Zealand.

"Sea lions were not able to withstand even low levels of sustained hunting pressure," said Dr Justin Maxwell, an Otago archaeologist.

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"Undetected bycatch may still be driving the decline," said associate professor Bruce Roberston, an Otago sea lion biologist. "Something the Government's recently released sea lion threat management plan (TMP) dismisses."

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.