The primary object of this study was to develop the control algorithm and program for automatic submersible buoy which is free to move vertically within the water column by adjusting weight and buoyancy forces by air control. The experiment was performed to validate the usefulness of the program in the indoor water tank. In the experiment, the automatic submerging and surfacing of the buoy were controlled by water-pressure gauge and air control system. The buoy is raised by injecting compressed air from a compressor and then is lowered by releasing the air. The submerging and surfacing characteristics of the buoy calculated with the numerical model were similar to measurements obtained with the experiment. It was concluded that the algorithm and program could be useful in analyzing various parameters and submerging mechanisms required to design new type of automatic submersible fish cage system.