Calyptrocalyx flabellatus is a small palm which has been recorded from several disjunct areas within Indonesian New Guinea: the Parfi and Wariori river valleys near Manokwari, the type collection site in the Arfak mountains, a site to the south of the Wandammen Peninsula, and the southern side of Lake Sentani, west of Jayapura. This disjunct distribution makes it difficult to estimate area of occupancy (AOO) and extent of occurrence (EOO) with any accuracy, as it is not known whether the palm is confined to these areas or whether its distribution is continuous between them. No numerical population data is available for this species. Herbarium specimen labels indicate that it is a species of lowland riverine or swampy areas below 160 metres asl; as such, there are hundreds of square kilometres of suitable habitat between the recorded sites for this species where targeted botanical collecting might reveal additional records. Calyptrocalyx is well-understood taxonomically, with a 2001 revision by Dowe and Ferrero, and the Palms of New Guinea project (Baker 2002) has meant that the palms of this region have been a research focus, including targeted collecting. This means that it is unlikely there are further extant herbarium specimens of this species which have not been seen by an expert. When calculating the AOO and EOO, the records from the Parfi River valley have been excluded as satellite images show this area is now oil palm plantations and the species is suspected to have been extirpated from this area. Although the forest is highly fragmented in the Lake Sentani area, some forest remains, particularly along rivers so it is possible that Calyptroclayx flabellatus persists in this region.

The AOO of 16–20 km² falls within the threshold values for the Endangered category under criterion B2, although this is fairly likely to be an underestimate given that New Guinea is botanically under-surveyed. The EOO of c. 78,000 km² exceeds the values for the threatened categories and there are between three and four locations, two of which are not thought to be subject to current or plausible future threat. At one of the collection sites at which the species is presumed to be extant, Lake Sentani, deforestation is evident. At other collection sites, and across much of the intervening range, habitat is inferred to remain intact, and it is unclear whether habitat loss at Lake Sentani is indicative of a continuing decline in habitat more broadly. However, the sites in the Wariori River could plausibly become threatened by logging or oil palm concessions operating in the vicinity in the near future, particularly as these sites lie outside any protected areas. If such concessions were to become operational, the species could become Critically Endangered in a short time. Given a restricted AOO, and plausible future threats that could result in a very high extinction risk, the species is precautionarily assessed as Vulnerable D2. It is suspected that the AOO applied here represents a significant underestimate, however, this is considered appropriate, particularly given that if the species were to be identified at additional sites subject to ongoing threat, then there is a high possibility that it would instead qualify as Vulnerable under criterion B2.

Calyptrocalyx flabellatus is endemic to New Guinea. The species has been recorded from several areas throughout Indonesian New Guinea (Dowe and Ferrero 2001). There are several records from the north-east of the Bird's Head Peninsula in the Manokwari District, one from the south of the Wandammen Peninsula and one record from near Jayapura. The recorded elevational range is from sea level to 160 metres asl.

No population information is available for this species, and the current population trend is unknown.

This species is a solitary palm that reaches 3 metres tall. Herbarium specimen label data suggests that Calyptrocalyx flabellatus is a species of both primary and disturbed lowland forests, with several records from alluvial forest and swamps.

The Calyptrocalyx flabellatus records from the lowlands in the Prafi River basin to the west of Manokwari are from an area which has now been logged and converted to palm oil plantations, and it is unlikely the species survives there. The records from the Wariori River area closer to Manokwari are from an area which appears to be continuous forest on satellite imagery, and does not have any logging or oil palm concessions recorded on Global Forest Watch (2022). However, the localities on the herbarium specimen labels (all collected 1994-95) are recorded as "Surya Company Timber Concession Area", "SP8 Transmigration Scheme" and "inland from Masni coastal logging camp" which suggests that potential threats from logging and settlement development exist in this region. The record from the southern part of the Wandammen Peninsula is from a region where the forest is more or less continuous and no obvious threats are present. The record west of Jayapura on the southern side of Lake Sentani is from an region where there is at least 50% forest loss visible on satellite imagery (Global Forest Watch 2023). The drivers of this forest loss are not known. The exact locality of the type specimen collection site in the Arfak Mountains is not clear, but there is much intact forest in this range.

This species is not known to be used.

None of the known sites for Calyptrocalyx flabellatus are inside protected areas, and there are no protected areas near any of these known sites (Global Forest Watch 2022). The species is present in 3 ex situ collections (BGCI 2023).