A magnetic disk apparatus of one of the embodiments stores read position dependency information on read signal quality of a data region at a first track and measures the read signal quality at a predetermined radial position in a second data region of a second track different from the first track. A positioning error of the second data region is determined based on the read position dependency information and the read signal quality at the predetermined radial position. Data is recorded in a recording target data region in a shingled recording so as to prevent data written in the second data region from being overwritten by data in a recording target data region adjacent to the second data region by using the determined positioning error.