A medical manipulator system including: a manipulator provided with an elongated portion, a movable portion which has one or more joints, and a driving portion which is disposed at a proximal end of the elongated portion and which drives the movable portion； a medical device having a channel that can accommodate at least a portion of the elongated portion and the movable portion； a manipulation input portion that generates an operation instruction for moving the manipulator between a treatment state in which the movable portion protrudes from a distal end of the channel and an accommodated state in which the movable portion is accommodated in the channel in accordance with a manipulation instruction input； and a notifying portion that notifies a situation in which the manipulator is shifting from the treatment state to the accommodated state.
