There is little specific information on the status or threats to whales of this species (Reeves et al. 2003). However, some are known to have been incidentally killed by whalers in Newfoundland, Iceland, and in the Barents Sea. A few entanglements in fishing gear (e.g., driftnets) have been documented. Waring et al. (2001) reported that for 1989-1998 observed bycatch in pelagic drift gillnets along the US East Coast amounted to 24 Sowerby's beaked whales. These were caught exclusively in the area from Georges Canyon to Hydrographers Canyon, along the continental shelf break and continental slope during July-October. This fishery has now been closed.

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).