An end-effector and a control method for tomato-cluster harvesting manipulator are proposed in this study. When fruit cluster harvesting is conducted, peduncle direction is necessary to cut, but is not easy to detect because peduncles are often occluded by leaves, stems and fruits. The end-effector needs to grasp the peduncle without its direction information. An end-effector which can surround main stem and can grasp and cut the peduncle by fingers was made as a trial. When a tomato cluster is transported into a container with the manipulator, both its transportation speed and vibration damping are required. Such a control problem is generally called a motion and vibration control (MOVIC). An input shaping method is one of the representative control methods for the MOVIC. It requires accurate natural frequencies of the manipulating target fruit cluster to damp the flexible vibration when the robot is accelerating the target. The tomato clusters, however, have individual variation with natural frequencies; hence, it is not easy to apply the input shaping method directly. To overcome this problem, identification method of natural frequency was combined with the input shaping method in the proposed method. This identification was based on real time sensing data from a machine vision and a force sensor and database of physical properties of the tomato clusters. Usefulness of the proposed method was verified through both numerical simulations and hardware experiments.