A method of the present invention is used to control a flying height of a head operable to read data from and write data to a disk of a recording medium housed in an enclosure. In this method, the head is positioned to a predetermined radial measurement location on the disk to obtain error information on errors in the positioning of the head. A frequency analysis is performed on the obtained error information. Disturbance information on errors caused by a wind disturbance is calculated from the frequency analysis result. Pressure information on an air pressure in the enclosure is calculated based on the calculated disturbance information. A control value for controlling a flying height of the head with respect to the disk is determined based on the calculated pressure information. The flying height of the head is controlled based on the determined control value.