Nominally protected areas in Papua are under threat from encroachment, logging and hunting. The northern cassowary Casuarius unappendiculatus is the largest frugivore of the lowland rainforest of New Guinea and is endemic to this region, and therefore it is an important conservation target and a potential flagship species. We investigated effects of habitat degradation on the species by means of distance sampling surveys of 58 line transects across five distinct habitats, from primary forest to forest gardens. Estimated cassowary densities ranged from 14.1 (95% CI 9.2–21.4) birds km−2 in primary forest to 1.4 (95% CI 0.4–5.6) birds km−2 in forest garden. Density estimates were intermediate in unlogged but hunted natural forest and in > 30 year-old secondary forest, and considerably lower in recently logged (< 3 years) forest. Cassowary abundance was positively correlated with canopy cover and with tree height and diameter, and negatively correlated with hunting traps and human trails. In generalized linear models cassowary abundance was best explained by the number of fruiting trees and potential water sources. The results suggest that although the northern cassowary is moderately tolerant of intermediate disturbance it is relatively intolerant of heavy disturbance such as intensive logging. To secure the populations of northern cassowary and of other large animal species in Papua, forest degradation needs to be addressed by enforcing regulations in existing protection forest and/or establishing new protected areas, such as wildlife reserves.