Like other members of the genus, almost nothing is known about the biology of the Pygmy Beaked whale. It occurs in deep waters, beyond the continental shelf, where it presumably undertakes long, deep dives, and spends relatively little time at the surface. However, off Peru, Pygmy Beaked Whales occur, perhaps seasonally, on the continental slope and shelf where they are caught in fishing nets (Reyes and van Waerebeek 2018).

The stomach contents of three individuals contained beaks of mesopelagic squids (Histioteuthidae, Gonatidae, and Cranchiidae), unidentified fish otoliths, and shrimp remains (Oplophoridae, Gammaridae; Reyes and Van Waerebeek 2018). Presumably, these prey were taken at moderate-to-great depths. Mean school size for 65 sightings in the eastern tropical Pacific was 2.3 individuals (SE = 0.14), with a range of 1-5 and a mode of 2 (Pitman and Lynn 2001). This sample may be biased, however, because it includes only schools with the distinctively patterned adult males present.

The Pygmy Beaked Whale is currently known from at least 36 specimens from Chile to central California, and there have been dozens of at-sea sightings of this distinctive species in the tropical and warm temperate eastern Pacific, including into the Gulf of California (Hamilton et al. 2008, Reyes and Van Waerebeek 2018). These records extend from about 43°S to 37°N, and observations at sea suggest that M. peruvianus occurs most commonly off western Mexico and is probably endemic to the eastern tropical Pacific. There are numerous records from Peru but to date only a single stranding record from Chile where it may be extralimital (Reyes et al. 1991, Sanino et al. 2007). A single stranding in New Zealand is also assumed to be an extralimital record (Baker and Van Helden 1999).

The species is listed in Appendix II of CITES. Research is needed to determine the impacts of potential threatening processes on this species.