A specially designed height finding radar, the navigation accuracy measurement system (NAMS) has been used for data collection on height keeping errors of aircraft. The height estimation accuracy of NAMS depends upon various parameters such as the radar cross section of a target, errors of sensors, the number of data acquisition, factors associated with its transmitter and receiver, and the geometrical situation between the antenna and the target. A computer simulation was carried out for estimating the height estimation accuracy based on the effective beam width. The results of the simulation are compared with the estimated measurement errors based on empirical data obtained by NAMS. This paper first describes the principle of height measurement. Then the simulation and the method of estimating height measurement errors based on NAMS data are described. Finally, the standard deviation of height estimation errors by both the simulation and empirical data are discussed herein.