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Airborne LiDAR scanning is a promising approach to providing high-resolution products that are appropriate for different applications, such as flood management. However, the vertical accuracy of airborne LiDAR point clouds is not constant and varies in space. Having a better knowledge of their accuracy will assist decision makers in more accurately estimating the damage caused by flood. Data producers often report the total estimation of errors by means of comparison with a ground truth. However, the reliability of such an approach depends on various factors including the sample size, accessibility to ground truth, distribution, and a large enough diversity of ground truth, which comes at a cost and is somewhat unfeasible in the larger scale. Therefore, the main objective of this article is to propose a method that could provide a local estimation of error without any third-party datasets. In this regard, we take advantage of geostatistical ordinary kriging as an alternative accuracy estimator. The challenge of considering constant variation across the space leads us to propose a non-stationary ordinary kriging model that results in the local estimation of elevation accuracy. The proposed method is compared with global ordinary kriging and a ground truth, and the results indicate that our method provides more reliable error values. These errors are lower in urban and semi-urban areas, especially in farmland and residential areas, but larger in forests, due to the lower density of points and the larger terrain variations.