A method of and apparatus for protecting data in a data storage system. A method of securely erasing data stored in a data storage system includes: determining whether a security-erase command is received together with a random number and an encrypted random number; decrypting the encrypted random number using a security-erase algorithm and an associated key when the security-erase command is received; determining whether the decrypted random number is identical to the received random number; and executing the security-erase command when the decrypted random number is identical to the received random number, and stopping the execution of the security-erase command when the decrypted random number is not identical to the received random number.