The paper presents the design of a hybrid controller used to control the movement of a ship in different operating modes, thereby improving the performance of basic maneuvers. This task requires integrating several operating modes, such as maneuvering the ship at low speeds, steering the ship at different speeds in the course or along the trajectory, and stopping the ship on the route. These modes are executed by five component controllers switched on and off by the supervisor depending on the type of operation performed. The desired route, containing the coordinates of waypoints and tasks performed along consecutive segments of the reference trajectory, is obtained by the supervisory system from the system operator. The former supports switching between component controllers and provides them with new set-points after each change in the reference trajectory segment, thereby ensuring stable operation of the entire hybrid switching controller. The study also presents designs of all controller components, which are done using a complex mathematical model of the selected ship, after its simplification depending on the type of controller. The developed control system was tested on the training ship Blue Lady and used to train captains at the Ship Handling Research and Training Center near Iława in Poland. The conducted research involved an automatic movement of the ship from one port to another. The performed transit route required the ship to leave the port, pass the water area, and berth at the port of destination. The study revealed good quality of the designed hybrid controller.