A magnetic storage apparatus has a reproducing head to reproduce information from a perpendicular magnetic recording medium that is recorded with servo information, eccentricity correction data and read/write data. The apparatus further has a filter part to filter a reproduced output of the reproducing head by filtering the servo information which has a differentiated waveform by a non-differentiating characteristic and by filtering the eccentricity correction data and the read/write data which have rectangular waveforms by a differentiating characteristic, a demodulating part to demodulate the servo information, the eccentricity correction data and the read/write data that are filtered by the filter part, and a servo system to carry out a control process including an eccentricity control based on the servo information and the eccentricity correction data that are demodulated.