Humans have probably harvested New Zealand Fur Seals for subsistence since first contact in both Australia and New Zealand. There is evidence that Polynesian colonization of New Zealand and harvest of seals led to declines and loss of colonies on the coast of the North Island. European sealers nearly exterminated the species in the 19th century, but due to protection, the species has rebounded to occupy most of its former range.

Trawl and other fisheries are a source of entanglement and drowning (Page et al. 2004). Tourism and disturbance at colonies can lead to disruption of breeding behaviour and site abandonment, although most colonies are on offshore islands and are relatively inaccessible.

Like all fur seals, New Zealand Fur Seals are vulnerable to oil spills because of their dependence on their thick pelage for thermoregulation (Gales 1991). New Zealand fur seals share most of their range with several other regularly occurring pinnipeds that show up irregularly as vagrants. They also come in close contact with domestic and feral animals and in some areas wild carnivores. Thus, they are at risk of transmission of infectious diseases like morbilliviruses.