A medical manipulator system including: a medical manipulator having a joint; an operating section having an operating system; and a control unit controlling the medical manipulator according to an operation applied to the operating section. The operating section includes a switch enters or releases a command. The control unit determines whether a deviation between the joint and the operating system exceeds a threshold while the command is entered, carries out a first motion for moving the joint by a displacement corresponding to the displacement of the operating system if the deviation is equal to or smaller than the threshold, carries out a second motion for approaching the joint to the operating system angle if the deviation exceeds the threshold, and stops the motion for approaching the joint to the operating system angle when the command is released when the deviation exceeds the threshold.