Because of their relatively low abundance, even small takes in localized areas could be significant. Although there is considerable controversy regarding the absolute level of declines, there is good evidence of large-scale reductions in many predatory fish populations (e.g., Baum et al. 2003, 2005; Sibert et al. 2006; Polacheck 2006) and over-fishing and collapse of several important “prey” fish stocks world-wide (e.g., Jackson et al. 2001). The effects of such fish population reductions and subsequent ecosystem changes on world-wide populations of pygmy killer whales are unknown but could result in population declines.

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

This species, like 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) and have been a part of multi-species unusual stranding events in Taiwan (Wang and Yang, 2006).

Pygmy killer whales have been killed directly in both harpoon and driftnet fisheries (Caribbean islands, Sri Lanka, Taiwan and Indonesia) and incidentally in various types of fishing gear (most areas of the species’ range).

A few individuals are known to be taken in drives and in driftnets in various regions, most notably Japan and Sri Lanka (Ross and Leatherwood 1994). Reports on the small-cetacean fisheries of St Vincent and Lamalera suggest that pygmy killer whales form a very small proportion of the catch and that catches probably have little impact on the subpopulations in those areas. In Sri Lanka, there is mortality of this species due to harpooning of dolphins for use as bait on long-lines for sharks, billfish, and other oceanic fishes (Ross and Leatherwood 1994).

Although they comprise less than 2% of all cetaceans in monitored by-catches in gillnet fisheries in Trincomalee, Sri Lanka and in villages on the south-west coast of Sri Lanka, this may amount to 300 - 900 pygmy killer whales each year (Ross and Leatherwood 1994). The numbers of animals killed incidentally in net fisheries, such as those in Sri Lanka, may be much higher than is so far documented, because monitoring of these widespread activities is incomplete. In the long term, such takes may have a significant impact on pygmy killer whales where their distribution overlaps with extensive gillnetting operations (Ross and Leatherwood 1994). Small incidental catches are known in fisheries in other areas including the Philippines and Taiwan (Ross and Leatherwood 1994, Dolar 1994, J. Wang pers. comm. 2007).

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.

This species does not appear to be particularly abundant anywhere that it has been sighted. In Hawaii, subpopulations appear to be small, and this, along with their limited movements, suggests the species may be particularly vulnerable to human impacts regionally.