Direct hunting has never been associated with this species. Entanglement in fishing gear, especially gillnets is probably the most significant threat.

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).

As a species potentially limited to temperate waters, the spade-toothed whale may be vulnerable to the effects of climate change as ocean warming may result in a shift or contraction of the species range as it tracks the occurrence of its preferred water temperatures (Learmonth et al. 2006). The effect of such changes in range size or position on this species is unknown.

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.