The effect of the atmospheric error in the spaceborne synthetic aperture radar (SAR) signal is more prominent in Malaysia due to its hot and wet conditions. Because the atmospheric error is believed to happen constantly in space and randomly in time, low-pass filtering in space and high-pass filtering in time is employed to measure it. However, with few scenes, the filtering technique's reliability in removing atmospheric error may be insufficient, leading to erroneous surface deformation. Therefore, an external atmospheric correction needs to be modelled to improve the accuracy of surface deformation. In this study, the atmospheric error correction was estimated from GPS and applied to the deformation analysis. The result shows that the atmospheric error level estimated from the filtering technique was -6.9 to 7.5 radians, while using GPS was -1.0 to 1.9 radians. After using the filtering process, the rate of deformation fell dramatically. However, compared to the reference deformation, the rate was too low, indicating that the filtering technique overstated the level of atmospheric error. At many data collections, the atmospheric correction calculated from GPS gave deformation values closer to the reference deformation. Hence, this study will help the researchers to model the atmospheric correction over the Malaysia region in future. © 2022 Institute of Physics Publishing. All rights reserved.