According to a magnetic disk apparatus of one embodiment, threshold voltages of memory cell transistors of a flash memory are set to a first section for a first value or to a second section for a second value. The second section is on a lower voltage side than the first section. The controller performs bit inversion of second data held in a volatile memory and writes the second data onto the flash memory when a power loss occurs while the second data corresponds to third data in which a number of the first values is larger than that of the second values. The controller writes the second data onto the flash memory without bit inversion when a power loss occurs while the second data corresponds to fourth data. The fourth data is data in which a number of the first values is smaller than that of the second values.