Direct hunting has never been associated with this species. Pervasive gillnet and longline fisheries throughout the species' range raises concern that some bycatch is likely. Even low levels of bycatch might cause unsustainable impacts on this naturally rare cetacean.

It is unknown if military, seismic or other loud noise-producing human activities resulted in the live stranding of a possible mother/calf pair in NE Taiwan (Wang and Yang 2006; Yang et al. 2008). However, “bubble-like lesions” were reported in at least one of these whales by Yang et al (2008). There is some evidence from Sri Lanka for occasional incidental or directed takes of animals identified as ‘bottlenose whales’ which are likely to be Indopacetus (Dayaratne and Joseph 1993).

Evidence from stranded individuals of several similar species of beaked whales indicates that they have swallowed discarded plastic items, which may eventually lead to death (e.g. Scott et al. 2001); this species may also be at risk.

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).

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