Indices or density estimators derived from counts of scat can be used as indirect measures of animal population density. An important issue in these studies is that scat decay rates vary across habitats and seasons. This is an often overlooked source of bias when using scat-based indices to make comparisons of relative abundance among sites or over time. I propose a simple method by which experimentally determined scat-persistence rates can be used as a correction factor in such indices. This measured persistence rate also serves as an important parameter in models that convert scat count data into population estimators. I test this method in a relative abundance survey of sambar deer (Cervus unicolor) for 6 sites across 2 national parks in northern Thailand. Using the correction factor changed the qualitative predictions of the abundance survey by altering the rank of the sites ordered by estimated sambar density. The ratio of corrected:uncorrected index values, which would stay constant across sites if there was no habitat-based variability in scat-persistence rates, changed by a factor of 2.7 when measured across sites and by 1.6 when measured across parks. This suggests that the application of persistence-rate correction factors could reduce the bias of scat-based index or estimator surveys by specifically accounting for decay rate variability.