No significant exploitation of southern bottlenose whales is known, and they have never been hunted on a large scale. Although never taken commercially, some southern bottlenose whales have been killed during whaling for research purposes. Some have also been incidentally killed in driftnets (Croxall and Nicol 2004). Recently several of this species have been recorded as bycatch of driftnet fishing in the Tasman Sea. Numbers taken annually are not known, however, (Jefferson et al. 1993).

This species, like other beaked whales, is likely to be vulnerable to loud anthropogenic sounds, such as those generated by navy sonar and seismic exploration (Cox et al. 2006).

Developing high-latitude fisheries, such as that for Antarctic toothfish, have the potential to reduce food available for large predators, such as Hyperoodon planifrons. That this fishery has a significant illegal component is an additional concern.

Predicted impacts of global climate change on the marine environment may affect southern bottlenose whales, although the nature of impacts is unclear (Learmonth et al. 2006).