A CT data processing apparatus and a CT data processing method capable of separating a subcutaneous fat region from a visceral fat region accurately and efficiently in CT data are provided. The CT data processing apparatus includes a center calculation part that calculates a body center 41 of an examinee on tomographic CT data, a start point setting part that identifies a vertebral column position 45 on the tomographic CT data and sets a start point on a muscular layer 37 on the opposite side of the vertebral column position 45 with respect to the body center 41, a muscular layer determination part that determines whether or not the muscular layer 37 is present in a first range 48, and when it is determined that the muscular layer 37 is present in the first range 48, further setting a point on the muscular layer 37 in the first range 48 as a new first reference point 47 and thus determining whether or not the muscular layer 37 is present in the first range 48, while moving the first reference point 47 from the start point 46, and a separation line calculation part that calculates a separation line so that the separation line passes through the first reference points 47.