During the 1950s and 1960s hunting with high powered rifles and motor boats was carried out on a large scale due to a rapid increase in the price of reptile leather. It was estimated that hundreds of thousands of crocodile were killed annually. In the Republic of Palau, Caroline Islands there was an official programme of extermination which occurred from 1966 to 1981 resulting in this species becoming extremely endangered. The preferred skins are from crocodiles between 0.75 and 1.50m in length, so larger crocodile are not the most commercially viable. The collection of eggs and young for farm rearing to marketable size poses a further threat.
Habitat loss reduces the prospects of recovery of populations already depleted by hunting.
In Australia the nesting habitat of Northern Territory is being destroyed by trampling by feral water buffaloes. The anchorage of floating mats of vegetation is being broken down so that the mat drifts away during the wet season on rivers such as the South Alligator. The second most important factor is the toleration of net fishing for barramundi well upstream of tidal river mouths and often right up into breeding areas. Another factor is animosity toward crocodiles, often directed at the Estuarine Crocodile, a large animal which eats humans and is aggressive when encountered near a nest. Eggs and meat are consumed in Papua New Guinea.