A capsule medical apparatus system includes a rotating magnetic field generation apparatus that generates a desired rotating magnetic field in three-dimensional directions, a capsule medical apparatus that includes a magnet and a needle for puncture that can be projected and retracted in a rotation direction of the rotating magnetic field and is rotated in the direction of the rotating magnetic field when the rotating magnetic field is applied to the magnet, a step-out operation detecting unit that detects a step-out operation by which the capsule medical apparatus is inversely rotated when a luminal surface is punctured with the needle, and a magnetic-field control instructing unit that controls the rotating magnetic field generation apparatus on the basis of a detection result performed by the step-out operation detecting unit.
