Ginkgo-toothed beaked whales have occasionally been taken by Japanese and Taiwanese whalers, and some have been caught in deepwater drift gillnets.

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). The use of active sonar from military vessels has been implicated in mass strandings of ginkgo-toothed beaked whales (Wang and Yang 2006; Yang et al. 2008).

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).