One Papuan language, Meriam, is spoken within the national borders of Australia, in the eastern Torres Strait.

To the west of New Guinea, the largest languages are Makasae in East Timor (100,000 in 2010) and Galela in Halmahera (80,000 reported 1990).

Although there has been relatively little study of these languages compared with the Austronesian family, there have been three preliminary attempts at large-scale genealogical classification, by Joseph Greenberg, Stephen Wurm, and Malcolm Ross.

[4] Since perhaps only a quarter of Papuan languages have been studied in detail, linguists' understanding of the relationships between them will continue to be revised.

Statistical analyses designed to pick up signals too faint to be detected by the comparative method, though of disputed validity, suggest five major Papuan stocks (roughly Trans–New Guinea, West, North, East, and South Papuan languages);[5] long-range comparison has also suggested connections between selected languages, but again the methodology is not orthodox in historical linguistics.

Other linguists, including William A. Foley, have suggested that many of Wurm's phyla are based on areal features and structural similarities, and accept only the lowest levels of his classification, most of which he inherited from prior taxonomies.

Similarly, several groups that do have substantial basic vocabulary in common with Trans–New Guinea languages are excluded from the phylum because they do not resemble it grammatically.

(Ross argues that open-class pronoun systems, where borrowings are common, are found in hierarchical cultures such as those of Southeast Asia and Japan, where pronouns indicate details of relationship and social status rather than simply being grammatical pro-forms as they are in the more egalitarian New Guinea societies.)

However, because of his more stringent criteria, he was not able to find enough data to classify all Papuan languages, especially many isolates that have no close relatives to aid in their classification.

Note that while this classification may be more reliable than past attempts, it is based on a single parameter, pronouns, and therefore must remain tentative.

[citation needed] Sorted by location north Irian: Sandaun Province: Sepik River: Bismarck Archipelago: Former isolates classified by Ross: Languages reassigned to the Austronesian family: Unclassified due to lack of data: Unaccounted for: Søren Wichmann (2013) accepts the following 109 groups as coherent Papuan families, based on computational analyses performed by the Automated Similarity Judgment Program (ASJP) combined with Harald Hammarström's (2012) classification.

The following families are identified by Timothy Usher and Edgar Suter in their NewGuineaWorld project:[20] In addition, poorly attested Karami remains unclassified.

Stephen Wurm stated that the lexical similarities between Great Andamanese and the West Papuan and Timor–Alor families "are quite striking and amount to virtual formal identity [...] in a number of instances".

[citation needed] William A. Foley (1986) noted lexical similarities between R. M. W. Dixon's 1980 reconstruction of proto-Australian and the languages of the East New Guinea Highlands.

[21] He believed that it was naïve to expect to find a single Papuan or Australian language family when New Guinea and Australia had been a single landmass for most of their human history, having been separated by the Torres Strait only 8000 years ago, and that a deep reconstruction would likely include languages from both.

However, Dixon later abandoned his proto-Australian proposal,[22] and Foley's ideas need to be re-evaluated in light of recent research.