Identifying areas of forest loss is a fundamental aspect of sustainable forest management. Global Forest Change (GFC) datasets developed by Hansen et al. (in Science 342:850–853, 2013) are publicly available, but the accuracy of these datasets for small forest plots has not been assessed. We used a forest-wide polygon-based approach to assess the accuracy of using GFC data to identify areas of forest loss in an area containing numerous small forest plots. We evaluated the accuracy of detection of individual forest-loss polygons in the GFC dataset in terms of a “recall ratio”, the ratio of the spatial overlap of a forest-loss polygon determined from the GFC dataset to the area of a corresponding reference forest-loss polygon, which we determined by visual interpretation of aerial photographs. We analyzed the structural relationships of recall ratio with area of forest loss, tree species, and slope of the forest terrain by using linear non-Gaussian acyclic modelling. We showed that only 11.1% of forest-loss polygons in the reference dataset were successfully identified in the GFC dataset. The inferred structure indicated that recall ratio had the strongest relationships with area of forest loss, forest tree species, and height of the forest canopy. Our results indicate the need for careful consideration of structural relationships when using GFC datasets to identify areas of forest loss in regions where there are small forest plots. Moreover, further studies are required to examine the structural relationships for accuracy of land-use classification in forested areas in various regions and with different forest characteristics.