Hubbs' beaked whale has occasionally been taken by Japanese whalers in several small cetacean fisheries. Whale meat products from this species are occasionally found for sale on the Japanese market (Dalebout et al. 2001). Incidental catches in drift gillnets occur sporadically off the coast of California.

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).

Evidence from stranded individuals of several similar species 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.

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).