A method, device and system for authenticating a programmable hardware device, such as a programmable hardware chip, and a command received by the programmable hardware device. A secure processor or other trusted source authenticates the programmable hardware chip by verifying, with the secure processor's own verification key, a random number sent to the programmable hardware chip and encrypted using a verification key embedded within the programmable hardware chip, since the nature of the encryption is such that only the original logic function that includes the verification key can encrypt the data correctly. A command received by the programmable hardware chip is authenticated by verifying that a command authentication token received by the programmable hardware chip is generated using the correct command authentication key and consequently verifying that the command is received from the secure processor, as only the party who has the command authentication key can encrypt the data correctly.