The validity of the genus Allonautilus Ward & Saunders, 1997 has been questioned (Harvey et al. 1999) but is supported by molecular data (Bonnaud et al. 2004, Bonacum et al. 2011). Allonautilus perforatus is known only from dead and drifted shells and is not considered a valid species by some authors. However, Ward and Saunders (1997) provide diagnostic characters for this species which is separated geographically from its sister species Allonautilus scrobiculatus by wide expanses of deep water known to serve as barriers to dispersal in nautilids. The type specimen is in the Academy of Natural Sciences, Philadelphia (Spamer and Bogan 1992) but a type locality is not designated.

Allonautilus perforatus is assessed as Data Deficient because its taxonomic validity has been questioned and, since it is known to science from drift shells only, very little is known about this species.

This species is known only from dead specimens: shells found washed up or in trade in Bali (Ward and Saunders 1997). It is assumed that the species occurs the waters around Bali, Indonesia however, there is too much uncertainty to be able to map its range. Its depth distribution is also unknown since the species is only known from empty drifted shells, however it is presumed to occur in the upper 700 m of the water column.

The population status and trends of this species are not known.

Nautiluses live on the steep sides of coral reefs and adjacent substrates (Jereb and Roper 2005, Saunders and Ward 2010). They are probably best characterised as mobile bottom-dwelling fore-reef scavengers and opportunistic scavengers (Jereb and Roper 2005, Saunders and Ward 2010, Dunstan et al. 2011a); they will also take small crustaceans such as crabs. They themselves are preyed upon by sharks and other fishes and, in some regions, by octopuses that drill into the shell (Saunders et al. 1991). Triggerfish attacks have been observed on numerous occasions (Saunders et al. 2011). A maximum of ten eggs are laid per batch, and experiments in aquaria have indicated that eggs take up to a year to hatch (Barord and Basil 2014). Juveniles hatch at 25–30 mm diameter growing to 6 or 7 cm diameter within a year. Whilst most research has been conducted on Nautilus pompilius sensu lato, it is likely that all nautilid species have similar longevity (15–20 years) exhibiting slow growth and low fecundity. Uneven sex ratios have been reported, based on fisheries catch data which showed ratios of between 20–30% female versus 70–80% male. Dunstan et al. (2011b) suggest, as have others previously, that these characteristics make nautiluses particularly vulnerable to over-exploitation.

Trade is the major potential threat to this species, as it is a threat to other nautilids, specifically since they are slow-growing, late-maturing (10–15 years of age), long-lived marine invertebrates (e.g. Dunstan et al. 2011a) and are lacking a larval phase which prevents them from having wider distributions (e.g. Dunstan et al. 2011b). According to the US Fish and Wildlife Service's second Federal Register Notice regarding the fifteenth regular meeting of the Conference of the Parties to CITES, more than 579,000 specimens of Allonautilus and Nautilus, approximately 99% of which were wild-harvested, were imported into the United States alone between 2005 and 2008. These specimens came mainly from the Philippines, Indonesia, and China with reports of Allonautilus increasingly found for sale in Indonesia.

Live animals of this species are not known to scientists. Export of nautilids is supposedly banned from Indonesia where this species occurs but imports apparently reach the USA from Indonesia. For example, there has been a prohibition on the harvest and sale of Nautilus pompilius since 1999 in Indonesia, however, the rarer A. perforatus was not protected at the time of a TRAFFIC study on nautilus trade (Freitas and Krishnasamy 2016). The CITES trade database only reports trade statistics for the family Nautilidae since it was listed in its entirety on CITES Appendix II in 2017. Since then, Indonesia has exported Nautilus products (jewellery) to the US for commercial trade (256 items in 2017), with some of these (31 items) reported as originating from wild-caught individuals and the remainder from confiscated or seized specimens; the species implicated were Nautilus belauensis and Nautilus pompilius (CITES Trade 2018). However, prior to that, seizures of nautilids have been reported from Indonesia, mainly from Bali, with sometimes hundreds of shells seized at a time (Freitas and Krishnasamy 2016). The rarer A. perforatus features less in trade as it is relatively hard to find (Freitas and Krishnasamy 2016).

The family Nautilidae was listed under CITES Appendix II in 2017 which includes all Nautilus and Allonautilus species. There has been a prohibition on the harvest and sale of Nautilus pompilius since 1999 in Indonesia, however, the rarer A. perforatus was not protected at the time of a TRAFFIC study on nautilus trade (Freitas and Krishnasamy 2016).