A method for correcting cross-track position errors in a digital printing system having a linear printhead includes printing a test target including a plurality of alignment marks. A data processing system is used to automatically analyze a captured image of the printed test target to determine a measured position for each of the alignment marks. The measured positions for the alignment marks is compared to reference positions to determine measured cross-track position errors. A cross-track position correction function is determined responsive to the measured position errors, wherein the cross-track position correction function specifies cross-track position corrections to be applied as a function of cross-track position. A corrected digital image is determined by resampling the image lines of a digital image responsive to the cross-track position correction function.