Object motion can introduce unknown phase shift and thus measurement error in multi-image phase-shifting methods of fringe projection profilometry. This paper presents a new method to estimate the unknown phase shifts and reduce the motion-induced error by using three phase maps computed over a multiple measurement sequence and calculating the difference between phase maps. The pixel-wise estimation of the motion-induced phase shifts permits phase-error compensation for non-homogeneous surface motion. Experiments demonstrated the ability of the method to reduce motion-induced error in real-time, for shape measurement of surfaces with high depth variation, and moving and deforming surfaces.