The IUCN Red List conservation status of Austral Pygmy-Owl is assessed as Least Concern (BirdLife International 2012). The global population size has not been quantified, but the species is reported to be the most abundant owl in Chile (Marks et al. 1999), and it is not considered to be a priority species for conservation (Pincheira-Ulbrich et al. 2008).
As is the case for almost all species of owls (regardless of the conservation threat), Austral Pygmy-Owl is included in Appendix II of CITES.