This article presents a new approach to the estimation of shift and rotation between two images from different kinds of imaging sensors. The first of the image is an orthophotomap that is created using optical sensors with georeference information. The second one is created utilizing a Synthetic Aperture Radar (SAR) sensor.The proposed solution can be mounted on a flying platform, and, during the flight, the obtained SAR images are compared with the reference optical images, and thus it is possible to calculate the shift and rotation between these two images and then the direct georeferencing error. Since both images have georeference information, it is possible to calculate the navigation correction in cases when the drift of the calculated trajectory is expected. The method can be used in platforms where there is no satellite navigation signal and the trajectory is calculated on the basis of an inertial navigation system, which is characterized by a significant error. The proposed method of estimating the navigation error utilizing Affine Scale-Invariant Feature Transform (ASIFT) and Structure from Motion (SfM) is described, and techniques for improving the quality of SAR imaging using despeckling filters are presented. The methodology was tested and verified using real-life SAR images. Differences between the results obtained for a few selected despeckling methods were compared and commented on. Deep investigation of the nature of the SAR imaging technique and noise creation character allows new algorithms to be developed, which can be implemented on flying platforms to support existing navigation systems in which trajectory error occurs.