Practically nothing is known about Hector's Beaked Whale. From the locations of the few strandings, most near oceanic islands or in areas with narrow continental shelves, we can infer that Hector's Beaked Whale normally occurs only in deep waters beyond the edge of the continental shelf, as do other members of the genus.

In the only known confirmed identification of this species alive at sea, a single individual was observed in shallow waters, nearshore in Western Australia – almost definitely atypical for the species (Gales et al. 2002).

Little is known of the diet, but Hector's Beaked Whales are known to feed on squid, and probably feed mainly on small mesopelagic squid and/or fishes, like most other mesoplodonts.

Hector's Beaked Whale occurs in cool-temperate waters of the Southern Hemisphere (Mead 1989, Van Waerebeek et al. 2010). The distribution records (essentially all strandings) are from southern South America (including Falkland Islands), South Africa, southern Australia, and New Zealand, suggesting a circumpolar range. The single specimen from southern Brazil is considered to be extralimital (Zerbini and Secchi 2001). There is only one confirmed live sighting a juvenile off southwestern Australia (Gales et. al. 2002).  Also two a male and female that stranding live in northern Argentina and then died (Cappozzo et al. 2005).

The species is listed in Appendix II of CITES. Research is needed to determine the impacts of potential threats on this species.