New Zealand Sea Lions were once more abundant, with a much more extensive range that included the North and South islands of New Zealand. The Maori people of New Zealand have traditionally hunted sea lions, presumably since first contact, as did Europeans upon their arrival much later. Commercial sealing in the early 19th century decimated the population in the Auckland Islands, but despite this, continued until the mid-20th century, when it was halted. The population may not have fully recovered from this period of overexploitation, although estimates of pre-exploitation population size are difficult to derive.

New Zealand Sea Lions have a highly restricted distribution, a small population, and most of the breeding activity is concentrated in two island groups in New Zealand's sub-Antarctic. This combination makes them vulnerable to disease outbreaks, environmental change, and human activities.

Commercial squid fishing near the two largest rookeries reported their first sea lion bycatch mortalities in 1978. In 1982, the fishery was moved at least 12 nautical miles away from the islands. However, this did not end mortality which from 1988 to 2007 ranged from 17-132 seals taken annually (Wilkinson et al. 2003, Chilvers 2008). Apart from direct mortality there is also the potential for prey competition and habitat modification from the fishing industry in the habitat of the New Zealand Sea Lion's breeding areas. Tourism at mainland sites and remote subantarctic islands can cause disruption to haul-out patterns and breeding activities.

Epizootic disease outbreaks at the Auckland Islands in 1998, 2002 and 2003 led to more than 50%, 33% and 21% early pup mortality respectively, and also led to mortalities of an unknown number of animals from other age classes during 1998. The source of the suspected bacterial agent and cause of the outbreak and subsequent mortality for the 1998 outbreak is unknown, however, the 2002 and 2003 outbreaks have been identified as cause by Klebsiella pneumoniae (Castinel et al. 2007).