Crocodylus novaeguineae was described in 1928 from northern New Guinea. Researchers working in the 1970s and 1980s noted that populations north and south of the central cordillera differed in nesting season, with northern animals nesting during the wet season and southern animals during the dry, alongside differences in size and skull proportions.
Those observations sat unresolved for decades. In 2019 the southern population was formally described as a separate species, Crocodylus halli, on the basis of morphological and molecular differences, restricting C. novaeguineae to the northern lowlands.
The northern species remains Least Concern. Papua New Guinea operates a long-running village-based programme in which eggs and juveniles are harvested under quota and skins are traded, an arrangement often cited as an early example of sustainable crocodilian use. As with all such schemes, its performance depends on monitoring, and independent verification of harvest sustainability is not continuous.