According to one embodiment, a magnetic disk apparatus includes an RW channel with an internal memory for processing data to be read/written from/to a magnetic disk, a transfer controller for controlling data transfer between a host apparatus and the RW channel, and a processor for controlling the RW channel and transfer controller. The processor reads, from the magnetic disk, predetermined area data including to-be-rewritten data, subjects the read predetermined area data to error correction processing in the RW channel, and stores resultant data in the internal memory. The processor rewrites, with rewrite data from the host apparatus, the to-be-rewritten data of the predetermined area data stored in the internal memory to update the predetermined area data, adds an error correction code to the updated data in the RW channel module, and writes resultant data to the magnetic disk.