Close-range photogrammetry methods are widely used for non-contact and accurate measurements of surface shapes. These methods are based on calculating the three-dimensional coordinates of an object from two-dimensional images using special digital processing algorithms. Due to the relatively complex measurement principle, the accurate estimation of the photogrammetric measurement error is a non-trivial task. Typically, theoretical estimations or computer modelling are used to solve this problem. However, these approaches cannot provide an accurate estimate because it is impossible to consider all factors that influence the measurement results. To solve this problem, we propose the use of physical modelling. The measurement results from the photogrammetric system under test were compared with the results of a more accurate reference measurement method. This comparison allowed the error to be estimated under controlled conditions. The test object was a flexible surface whose shape could vary smoothly over a wide range. The estimation of the measurement accuracy for a large number of different surface shapes allows us to obtain new results that are difficult to obtain using standard approaches. To implement the proposed approach, a laboratory system for the error estimation of close-range photogrammetric measurements was developed. The paper contains a detailed description of the developed system and the proposed technique for a comparison of the measurement results. The error in the reference method, which was chosen to be phasogrammetry, was evaluated experimentally. Experimental testing of the stereo photogrammetric system was performed according to the proposed technique. The obtained results show that the proposed technique can reveal dependencies that may not be detected by standard approaches.