Monitoring rare and elusive species for effective management and conservation is particularly challenging and often demands the development of specialized techniques. Scat surveys have been applied to monitor a variety of rare species but relatively little attention has been given to the development of appropriate sampling designs. To determine if scat surveys could be applied to compare the distribution of species across three habitats of a fragmented region in the Brazilian Amazon, the removal of human (n = 27) and jaguar (n = 27) scat samples in forest, riparian corridor and pasture habitats was recorded for 24 hours. Dung beetles were responsible for removing the majority of samples (71%) and a generalized linear mixed effect model revealed significant influence of habitat and scat type on removal probability, with forest and riparian corridors having higher removal compared with samples in pasture habitats. Although non-invasive scat surveys can potentially address fundamental broad-scale conservation and management questions, our results demonstrate that scat surveys in the tropics must account for differences in scat removal rates between habitats and target species before conclusions can be drawn regarding patterns of habitat use.