Unwanted oscillations caused by the operator-commanded motions lower the capable operating speeds and degrade the safety of dual cranes moving distributed-mass payloads. Mounting numbers of works have been devoted to the dynamics and control of dual cranes. However, few studies have been dedicated to the accurate estimation of natural frequency, which is a critical factor for controlling the dual cranes. This paper develops a new method to predict the natural frequency of dual planar cranes with different cable lengths. Furthermore, a modified extra-insensitive (MEI) input shaper is proposed to suppress the oscillations of the payload swing and pitch in the dual cranes. The MEI shaper has good robustness to large changes in the frequency, and has good performance in the jerk limitation. Simulated and experimental investigations are performed on small-scale dual cranes transporting a slender beam to validate the system dynamic behavior and the effectiveness of the MEI shaper.